RiceWiki - User contributions [en]

Os04g0413500

2014-06-06T04:00:50Z

Lq2014rice: /* Knowledge Extension */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

3.'''''GIF1''''' (grain incomplete filling 1) is filling defective mutants screened from flowers 11 mutant strain , with mutant morphology and seed rate on the performance of normal, but the filling degree lower than the wild type, grain starch granules arranged loose, chalky whiteness, the final grain weight lower than 24% of wild-type. Starch, amylopectin and amylose content was significantly lower than that of wild-type.

4.RDesueaprchl iacrtiacletion and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication.

[[File:c1.jpg]]

'''Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci'''. '''(A)''' The N-J phylogenetic tree constructed by MEGA program based on alignment of the DNA sequences of the 8 CWI genes of rice and CWI genes in other species, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and the recently released maize and sorghum genomes. Note that the rice GIF1 and OsCIN1 genes were paralogous within two subgroups. '''(B)''' Synteny between the GIF1 and OsCIN1 genome regions is illustrated schematically with homologous genes, indicating their duplication event.

[[File:d1.jpg]]

'''Different GIF1 and OsCIN1 expression patterns.''' '''(A)''' Levels of the GIF1 and OsCIN1 transcripts were detected by RT-PCR in different tissues. '''(B)''' Levels of the GIF1 and OsCIN1 transcripts during grain filling. Note that OsCIN1 was constitutively expressed in developing grains. The experiments were repeated twice with similar results, Ubi-1 was used as a loading control for RT-PCR. DAP, day after pollination; Cyc, PCR cycles.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:D1.jpg

2014-06-06T03:59:09Z

Lq2014rice:

File:C1.jpg

2014-06-06T03:58:50Z

Lq2014rice:

Os04g0413500

2014-06-06T03:58:02Z

Lq2014rice: /* Knowledge Extension */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

3.'''''GIF1''''' (grain incomplete filling 1) is filling defective mutants screened from flowers 11 mutant strain , with mutant morphology and seed rate on the performance of normal, but the filling degree lower than the wild type, grain starch granules arranged loose, chalky whiteness, the final grain weight lower than 24% of wild-type. Starch, amylopectin and amylose content was significantly lower than that of wild-type.

4.RDesueaprchl iacrtiacletion and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication.

[[File:c1.jpg]]

Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci. (A) The N-J phylogenetic tree constructed by MEGA program based on alignment of the DNA sequences of the 8 CWI genes of rice and CWI genes in other species, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and the recently released maize and sorghum genomes. Note that the rice GIF1 and OsCIN1 genes were paralogous within two subgroups. (B) Synteny between the GIF1 and OsCIN1 genome regions is illustrated schematically with homologous genes, indicating their duplication event.

[[File:d1.jpg]]

Different GIF1 and OsCIN1 expression patterns. (A) Levels of the GIF1 and OsCIN1 transcripts were detected by RT-PCR in different tissues. (B) Levels of the GIF1 and OsCIN1 transcripts during grain filling. Note that OsCIN1 was constitutively expressed in developing grains. The experiments were repeated twice with similar results, Ubi-1 was used as a loading control for RT-PCR. DAP, day after pollination; Cyc, PCR cycles.

[[File:e1.jpg]]

Phenotypes of OsCIN1-OE and GIF1-OE plants. (A) The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector control (left). (B) The OsCIN1-OE plants produced grains completely filled (right). (C) Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). (D) The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same time. (E) The GIF1-OE plants grew dwarfing in comparison with the control. (F) The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Talk:Os04g0413500

2014-06-06T03:16:32Z

Lq2014rice: Created page with "Increasing the weight of each one rice - called grain filling - has been and still is the goal of people to choose rice. Previous studies have isolated a gene for a number of ..."

Increasing the weight of each one rice - called grain filling - has been and still is the goal of people to choose rice. Previous studies have isolated a gene for a number of QTL, however, Wang et al reported that a key regulator of the whole process, a method of transforming the cell wall enzyme, capable of controlling the rice tissues, including the number of grains of starch. They found that, GRAIN INCOMPLETE FILLING 1 (GIF1) using a mutant screen, while the GIF1 implanted genetically modified rice, thus confirming its function. Wang, who is also on the history of this gene has been studied, and thus prove its promoter region in the process of domestication of rice has undergone a sweeping choice, it's like people expected. Further studies will now focus on this area in order to make greater use of this gene.

Os04g0413500

2014-06-06T03:12:00Z

Lq2014rice: /* Knowledge Extension */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

3.'''''GIF1''''' (grain incomplete filling 1) is filling defective mutants screened from flowers 11 mutant strain , with mutant morphology and seed rate on the performance of normal, but the filling degree lower than the wild type, grain starch granules arranged loose, chalky whiteness, the final grain weight lower than 24% of wild-type. Starch, amylopectin and amylose content was significantly lower than that of wild-type.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T03:11:24Z

Lq2014rice: /* Knowledge Extension */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

3.GIF1 (grain incomplete filling 1) is filling defective mutants screened from flowers 11 mutant strain , with mutant morphology and seed rate on the performance of normal, but the filling degree lower than the wild type, grain starch granules arranged loose, chalky whiteness, the final grain weight lower than 24% of wild-type. Starch, amylopectin and amylose content was significantly lower than that of wild-type.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T03:02:13Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:B1.jpg

2014-06-06T03:01:34Z

Lq2014rice:

File:A1.jpg

2014-06-06T02:59:53Z

Lq2014rice:

Os04g0413500

2014-06-06T02:59:03Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]] [[File:a1.jpg]] [[File:b1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:56:56Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:55:31Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:a.jpg]][[File:b.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:54:14Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:abcdef.jpeg ]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:53:47Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:abcdef.jpeg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:52:00Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:abcdef.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:49:00Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:Figure_1.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:46:52Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

[[File:Example.jpg]] [[File:Example.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:34:38Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:34:17Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]
'''Figure 1''' Grain-filling and sugar content of gif1 mutant and wild-type rice.'''(a,b)'''Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:32:50Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]
'''
''''''Figure 1''' Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''''''''(a,b)''' Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:32:06Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.''''''(a,b)''' Grains of gif1 '''(a)''' and wild-type '''(b)''' rice at 25 DAP (see Supplementary Fig. 1 for seed development). '''(c,d)''' White grains of gif1 '''(c)''' and wild-type '''(d)'''rice. '''(e,f)''' Scanning electron microscope analysis of gif1 '''(e)''' and wild-type '''(f)'''grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. '''(g)''' Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. '''(h–j)''' Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:30:30Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''Figure 1 Grain-filling and sugar content of gif1 mutant and wild-type rice.
'''(a,b)''' Grains of gif1 '''(a)''' and wild-type (b) rice at 25 DAP (see Supplementary Fig. 1 for seed development). (c,d) White grains of gif1 (c) and wild-type (d)
rice. (e,f) Scanning electron microscope analysis of gif1 (e) and wild-type (f)grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, 1,500. Scale bars represent 10 mm. (g) Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. (h–j) Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:29:36Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''Figure 1 Grain-filling and sugar content of gif1 mutant and wild-type rice.
(a,b) Grains of gif1 (a) and wild-type (b) rice at 25 DAP (see Supplementary Fig. 1 for seed development). (c,d) White grains of gif1 (c) and wild-type (d)
rice. (e,f) Scanning electron microscope analysis of gif1 (e) and wild-type (f)grains. Starch granules developed abnormally and were packed loosely in gif1 grains. Magnification, �1,500. Scale bars represent 10 mm. (g) Grainfilling process (weight in grams of 1,000 brown grains) of gif1 and wild-type (WT) rice. (h–j) Sucrose, glucose and fructose contents of gif1 and wild-type grains. Data in g–j are shown as means ± s.e.m.

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:27:14Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice.

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:26:57Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].Consistently,amylose and amylopectin levels were significantly lower in gif1 than in wild-type rice

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:25:36Z

Lq2014rice: /* Grain-filling and sugar content of gif1 mutant VS. Wild-type rice. */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules.The reduced filling rate resulted in reduced weight of gif1 grains starting 3 d after pollination (DAP); the final grain weight of the gif1 mutant was B24% lower than that of wild type rice at 30 DAP[2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:15:13Z

Lq2014rice: /* Function */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.
GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch[1,2].

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:13:36Z

Lq2014rice: /* Function */

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain. GIF protein is capable of controlling rice tissues, including the number of grains of starch. Modern cultivated GIF1 gene rice has tissues strict specificity, which can in favor of grain filling and improve rice yields.GIF1 gene is responsible for controlling invertase (invertase) activity, wihch is located on the cell wall. Invertase can put sugar into a substance used in the manufacture of starch.

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T02:01:34Z

Lq2014rice:

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.

2. China National Rice Research Institute, 359 TiyuChang Road, Hangzhou 31006, China.

3. Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China.

4. School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

6. College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T01:55:07Z

Lq2014rice:

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

2. China National Rice Research Institute.

3. Zhejiang Academy of Agricultural Sciences.

4. School of Life Sciences, Fudan University.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania.

6. College of Agriculture, South China Agricultural University.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0413500

2014-06-06T01:54:38Z

Lq2014rice:

GIF1 gene was located on chromosome 4, the exact size of the interval to 32kb. RT-PCR analysis and functional complementation experiments show, Os04g33740 gene that GIF gene, cDNA full length 2089bp, containing the protein product of seven exons encoding 598 amino acids, and gif1 mutant allele occurs one base missing. Analysis showed that GIF is a cell wall converting enzyme protein, with sequence highly similar to corn and tomatoes LIN5 Mn1.

==Annotated Information==
===Function===
'''''GIF1'' ((grain incomplete filling 1))''' plays an important role in crop cultivation which controlling crop grain-filling remain elusive. The cultivated ''GIF1'' gene shows a restricted expression pattern during grain-filling compared to the wild rice allele. Fine mapping with introgression lines revealed that the wild rice ''GIF1'' is responsible for grain weight reduction[2]. The overexpression of ''GIF1'' driven by its native promoter increased grain production. It is suggested that ''GIF1'' is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement[2]. ''GIF'' protein could control rice tissues, including the number of the starch grain. The ''GIF1'' gene in modern cultivated rice is specifically expressed in strict organization which good for grain filling, increasing the yield of rice[2].The ''GIF1'' gene is responsible for controlling Sucrose Enzyme (enzyme) activity which is located in the cell wall. the ''GIF1''could converse sucrose to starch material for manufacturing.The Sucrose Enzyme play an important role in starch formation. If the Sucrose Enzyme is inactive, rice plants might not make full edible grain.

===Grain-filling and sugar content of ''gif1'' mutant VS. Wild-type rice.===

'''Grain-filling and sugar content of ''gif1'' mutant:''' The mutant was morphologically normal, with normal seed setting. It showed slower grain-filling than wild-type rice [2].

[[File:a.jpg]] [[File:Figure_1.jpeg‎ ]]

[[File:e.jpg]] [[File:c.jpg]]

'''Figure 1 Grain-filling and sugar content of gif1 mutant VS. Wild-type rice.'''

'''Wild-type rice:''' The gif1 mutant also showed markedly more grain chalkiness as a result of abnormally developed and loosely packed starch granules [2].

===Expression===
1. ''Wang et al''. investigate the site of ''GIF1'' action using a pGIF1- β –glucuronidase (GUS) reporter transgene (pGIF1-GUS). GUS activity was mainly detected in growing roots, the node and the rapidly elongating zone of the internode, similar to its transcript accumulation. Particularly during early grain-filling, strong GUS activity was observed in the ovular vascular trace end of the grain at 3 and 5 DAP. It is proposed that propose that the restricted expression pattern of the GIF1 gene in the ovular vascular trace is the key to increased grain weight. Consistent with our interpretation, transgenic rice plants that ectopically expressed the cultivated ''GIF1'' gene from the rice ''Waxy'' promoter also had smaller grains [2](Figure 2).
An extensive microarray survey of gene expression indicates that many genes encoding proteins involved in sugar and energy metabolism have higher expression levels in O. rufipogon than in cultivated rice. The restricted expression pattern of ''GIF1'' in the vascular bundle should facilitate sucrose unloading favoring grain-filling, whereas the wild rice ''GIF1'' allele might promote energy metabolism [2].

[[File:j.jpg]]

'''Figure 2''' Expression pattern and localization of GIF1. '''(a,b)''' GUS activity in the growing root '''(a)''' and the node and elongating zone of the internode '''(b)'''.'''(c,d)''' GUS activity in developing grains was restricted to the ovular vascular trace (OV) end at 3 DAP (c) and 5 DAP (d). '''(e)''' GUS activity in the OV and lateral stylar vascular trace (SV) of grains at 10 DAP. '''(f)''' GUS activity in the OV at 20 DAP. '''(g)''' Cross-section of the grain at 10 DAP. '''(h)''' Boxed area in g observed under a microscope, showing GUS activity in the OV. NP, nucellar projection. '''(i)''' GIF1 transcript levels detected by RT-PCR. UBI1 was used as a loading control. The analysis was repeated twice with similar results. '''(j)''' GIF-GFP fusion protein localized to the cell wall in a transgenic rice root tip. Arrow indicates plasmolysis. Scale bars represent 3 mm (c–g) or 100 mm (h).

2. ''Wang et al.'' used microarray analysis to examine the regulation of genes involved in sugar metabolis and proposed that sucrose partitioning is altered by the gif1 mutation, leading to lower sucrose levels in the gif1 grain, as similarly reported for carrot [2].

3.Real-time PCR quantitatively by ''Wang et al.''confirmed expression levels of the wild and cultivated alleles.Similarly elevated expression of wild rice ''GIF1'' was found in other tissues of the introgression lines (data not shown). These results strongly suggest that ''GIF1'' is a domestication gene and that the restricted expression pattern of the cultivated ''GIF1'' gene was caused by nucleotide changes in its promoter during rice domestication [2].

4. The mapping experiment made by ''Wang et al.'' revealed that the wild rice ''GIF1'' is most likely to be the gene that decreases grain weight in the introgression lines. The further analyzed the effect of cultivated alleles on grain-filling using three introgression lines in a recurrent Huajingxian 74 (indica) background with two japonica alleles and one indica allele with distinct origins (in total, two japonica alleles and two indica alleles). It could be proved that these introgression lines showed no difference in grain weight, suggesting that the cultivated rice alleles of indica and japonica have the same effect on grain-filling.

===Knowledge Extension===

1. Grain filling is the process of increasing the weight of every grain of Rice. The grain filling is also the aim which proposed by human. ''Wang et al.'' made a research of history of this gene, and proved that its promoter region chose to clean in the process of domestication of rice just as the expectation of people[2]. More researches would concentrate this area which would be helpful in using this gene.

2. There is found that ''GIF1'' and ''OsCIN1'' is a pair of duplication which experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity and provided a vivid example for evolution of genetic novelties in a model crop[1]. Differential biological functions of ''GIF1'' and ''OsCIN1'':

'''''GIF1'':''' ''GIF1'' is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage[3]. Overexpression of the ''GIF1'' gene produced plants with marked defects both in grainfilling and development, indicating that over-activity of the ''GIF1'' enzyme disrupts sugar homeostasis, a process important to normal grain and plant development.

'''''OsCIN1'':''' ''OsCIN1'' has lower CWI activity compared to ''GIF1'' in the transgenic plants. Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting. Interestingly, ''OsCIN1'' might be involved in pathogen defense and stress response[4]. It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development[5][6], which are also involved in stress responses[1].（Figure 3）

[[File:yyy.jpg]]

Figure 3 Phenotypes of OsCIN1-OE and GIF1-OE plants. '''(A)''' The GIF1-OE plants produced badly-filled grains (right), compared to the empty vector
control (left). '''(B)''' The OsCIN1-OE plants produced grains completely filled (right). '''(C)''' Smaller seeds of the GIF1-OE plants (right), compared to the empty vector control (left). '''(D)''' The OsCIN1-OE seeds exhibited preharvest sprouting, while the control seeds did not germinate on panicle at the same
time. '''(E)''' The GIF1-OE plants grew dwarfing in comparison with the control. '''(F)''' The OsCIN1-OE plants were morphologically similar to the control.

==Labs working on this gene==
1. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

2. China National Rice Research Institute.

3. Zhejiang Academy of Agricultural Sciences.

4. School of Life Sciences, Fudan University.

5. Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania.

6. College of Agriculture, South China Agricultural University.

==References==
[1] Wang E., Xu X., Zhang L., et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evolutionary Biology 2010, 10: 108

[2] Wang E., Wang JJ., Zhu XD., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics 2008, 40(11): 1370-1374.

[3] Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH: Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 2008, 40:1270-1274.

[4] Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS: Molecular cloning and expression analysis of the cell wall invertase gene family in rice (Oryza sativa L). Plant Cell Rep 2005, 24:225-236.

[5]Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X,Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 2009, 106:2071-2076.

[6]Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004, 38:615-643.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0413500|
Description = Similar to Cell wall invertase 2|
Version = NM_001059283.1 GI:115458295 GeneID:4335790|
Length = 4751 bp|
Definition = Oryza sativa Japonica Group Os04g0413500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:20444480..20449230|
CDS = 20444531..20444735,20445379..20445387,20445875..20446755,20447145..20447306,20448058..20448317 ,20448426..20448516,20448803..20448991|
GCID = <gbrowseImage1>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:20444480..20449230
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatgatccgaacgcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctgatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaa</cdnaseq>|
AA = <aaseq>MGVLGSRVAWAWLVQLLLLQQLAGASHVVYDDLELQAAATTADG VPPSIVDSELRTGYHFQPPKNWINDPNAPMYYKGWYHLFYQYNPKGAVWGNIVWAHSV SRDLINWVALKPAIEPSIRADKYGCWSGSATMMADGTPVIMYTGVNRPDVNYQVQNVA LPRNGSDPLLREWVKPGHNPVIVPEGGINATQFRDPTTAWRGADGHWRLLVGSLAGQS RGVAYVYRSRDFRRWTRAAQPLHSAPTGMWECPDFYPVTADGRREGVDTSSAVVDAAA SARVKYVLKNSLDLRRYDYYTVGTYDRKAERYVPDDPAGDEHHIRYDYGNFYASKTFY DPAKRRRILWGWANESDTAADDVAKGWAGIQAIPRKVWLDPSGKQLLQWPIEEVERLR GKWPVILKDRVVKPGEHVEVTGLQTAQADVEVSFEVGSLEAAERLDPAMAYDAQRLCS ARGADARGGVGPFGLWVLASAGLEEKTAVFFRVFRPAARGGGAGKPVVLMCTDPTKSS RNPNMYQPTFAGFVDTDITNGKISLRSLIDRSVVESFGAGGKACILSRVYPSLAIGKN ARLYVFNNGKAEIKVSQLTAWEMKKPVMMNGA</aaseq>|
DNA = <dnaseqindica>52..256#900..908#1396..2276#2666..2827#3579..3838#3947..4037#4324..4512#atcctcctctcctcttctcgctctcacttcttgtgcccaagtgtgagagcaatgggagttcttggtagtagggtcgcttgggcatggctggtccagctgctgctgctccagcagctcgccggagcgtcgcacgtcgtctacgacgacctcgagctgcaggcggctgctaccacagcggacggcgtgccgccgtccatcgtcgactctgagctccggactgggtatcacttccagccacccaagaactggatcaatggtaatgtgaactaactgaaatgttgccaacttgccattgttcatgccagaacgccggtcaggccgtatgatttgcaggtcatagggcaccacttgtggttgtggatactggatagatgagcaaagggaacagagtgctctgttcttgagaattgagacgcagaatcgtgcagagtaactagtacagttttgacgacgttgttgtgtagaacatcacctgaactaaatggctcaacttgagtaatttatagtcagagttgaaaatattgacatcatagtcatatcaaatgtttggcacacaacataaattacggacagtacactaaggcatcagtttttatgtccattttgtcgggtcagctagtagagtcaacgttagcacccacgcggtcacgctgaaagaagtagcttcagaagcatctcacagtaaactactgagagtttgccatctctttttcatgaagctcacacttagtcccttcgaactgttaacagatgtactaccttgttctacttttcttgctaatgattcttgtgacaaggcttagtcctaaccggcaattttcttgtgcaattatttggtgggggtgtgctctgctctacactgtgattgctgctgcgtcatcaacattggaaacccgcagatccgaacggtacgtcgttttcccaccctttataatatatcctgtcacgaatctctgtctactagtagtagtagtagtagtactagaacttttatgccttgcaacttgcaatttcgttgtacgggagaggactgtagttagtgacgcctttcatggtaggattaaaggttcaaagcacattttagcacgaaaatggtaggcgcactgggactccacatgcaggcttgcttgtcgaccgtggggtacctagcccctaccacggctgatgaccacaaagttcagaaaatcttaacttcctctcagaaagggaattagccaaaagttcacctttttctcgtacgaaatgaagcatctatagttctataattaatcgtgagcagtgtagagaaaaatgcaatgtacacgcgcgattaaactgaaatggtaattgatttcaatgtactactaagactgaagatcatttcttgatttggtgaaactgaacgggtgcatgcagcgccgatgtactacaaggggtggtaccatctgttctaccagtacaaccccaagggcgccgtgtgggggaacatcgtgtgggcgcactcagtgtcacgtgacctcatcaactgggtggcgctcaagccggccatcgagcccagcatcagggccgacaagtacggctgctggtcggggtcggcgacgatgatggccgacgggacgccggtgatcatgtacaccggcgtcaaccgccccgacgtcaactaccaggtgcagaacgtggcgctgccgaggaacgggtcggacccgctgctgcgcgagtgggtgaagcccggccacaacccggtgatcgtgcccgagggcggcatcaacgcgacgcagttccgcgacccgaccaccgcgtggcgcggggccgacggccactggcggctgctcgtcggcagcctcgcggggcagtcccgcggcgtggcgtacgtgtaccggagcagggacttccggcggtggacgcgcgcggcgcagccgctgcactcggcgcccacggggatgtgggagtgcccggacttctacccggtcaccgcggacggccgccgcgagggcgtcgacacctcgtccgccgtcgtcgacgccgccgcctcggcgcgcgtcaagtacgtgctcaagaacagcctcgacctgcgccggtacgactactacaccgtcggaacgtacgaccggaaggccgagcggtacgtgccggacgaccccgccggcgacgagcaccacatccgctacgactacggcaacttctacgcctccaagacgttctacgacccggcgaagcgccgccgcatcctctggggatgggccaacgagtccgacaccgccgccgacgacgtggccaagggctgggccggaatccaggtaattaaccgcacgtcctgactgcatacgtgcatgccatttacgtgtccaccatgcatgctgccatcttcagatagtcaatatcaccatatactccctccgttctaaaatgtttaacaccattgactttttagcacatgtttgaccgttcgtcttattaaaaaaatatgaaatatataaaactatatgtatacataaaagtatatttaacaatgaatcaaatgatatgaaaagaacaaataattacttaaattttttgaataagacgaatggtgtcaagtattttgaaaaaagagagtatatcttaaaagtcaaatggaacaacactagcagctcaattttgctggtaatctttgattgaatcgtgtgtttgtgatgtgatgttttaggcgattccgaggaaagtgtggctggacccaagtgggaagcaactgttgcagtggccaatcgaggaggtcgagaggctgagagggaagtggccggtcattctcaaggacagggtggtcaagccaggggaacacgtcgaggtgaccgggctacaaactgcacaggtattcctttttgcatctgtaattctgtaaaactattttttttaccccaaaagggcattcgaataaaactgctcacacatccatggttctgtgcatgacagtagtaattattaataagttatcctgtttgttttgctgtgtcctggaccgatctttatcttatctggcacgcctgaagttgtgtccagtgtgcagtgcccactgaacaccacctactacgtgtgccgtgtcgctttcttctcgtccccttttaccatctcctgcacactttgctcgtacttaactgatctcactgattctctcgtcatccgcgcatgtcacgtacaacttccaggttgcagcgtgattagtgcacatatcactaagacactaaacaacataattagagagatagttaaggagctcaattaatgtgctttgttggtgacgtacgtgagtaggagctgtgatctctgatagcaagtttaatagtatagctaactactggctctaaattatctatagtcaatctaataataaattcatataatagttacctataaacatatactaaataattaatacatggttccacatgtcatacacatatgcatcttaaagtccgtactataatttgctgtaaatctatagcttgttgtttttctctctcctcttttatctcctcgatcgaaatgtgtttatagctggcttatagtgtgctattgtccctggtctgatgaagtgatcatgcattctgtttggtggggtgcaggctgacgtggaggtgagcttcgaggtggggagcctggaggcggcggagcggctggacccggcgatggcgtacgacgcgcagcggctgtgcagcgcgcggggcgccgacgcgaggggcggcgtggggccgttcggcctgtgggtgctcgcgtccgcggggctggaggagaagaccgccgtgttcttcagggtgttcaggccggcggcgcgcggcggcggcgccggcaagcccgtcgtgctcatgtgcaccgaccccaccaagtacgtgcggcttttgcactttatcggtgattgatcgcactacacaataaacaaaatattgccttgactccgtttactgattttttggtatggtgcgtatgcgtgcaggtcatcgcgcaacccgaacatgtaccagccgacgtttgcagggttcgttgacacggacatcaccaacgggaagatatctctgaggagcctggtacgtaataggaccaaattatcgggaaaaaaggaaaatgttgcatgacggtatcccgttcggataaaattatacctcttaaatattgtccgatacctaataaatattaattggctaataaactatttgaatgggatgatatctttgaggtatcgtctgatacctatctgataggtacctcataggtatcacctcgtccgaacgggttactgttttataacattcatctggaaaaggttcataaattgtagaatatgttttgatatcttgtgtctctcttgtgcagatcgacaggtcggttgttgagagcttcggggctggaggaaaggcgtgcatcctgtcgagggtgtacccgtcgctggccatcggcaagaacgcgcgcctttacgttttcaataacgggaaggcggagatcaaggtgtcgcagctcaccgcgtgggagatgaagaagccggtcatgatgaatggagcctaaacaatatttgaaattgagagagatagatgcaatgcatgatgagaactaccttcagtagctagctagatttttgagtttcagcggaaaagaaaaaactgattgcccttaattatgtgctaaatcatgcccccttgtgtaaaatggtttcagtcacacgtgtcgtatgcatatgtaccaaggggacagtttgaatgcatggatgccattaggactaataaagattgatgctagtataaccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059283.1 RefSeq:Os04g0413500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]