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Os09g0441900

2014-06-10T16:23:55Z

Laughin: /* Function */

The rice ''Os09g0441900'' was identified as ''DEP1'' (DENSE AND ERECT PANICLE1) and ''qPE9-1'' respectively in 2009 by researchers from China<ref name="ref1" />.(in chronological order).
==Annotated Information==
===Function===

*Natural variation at the ''DEP1'' locus enhances grain yield in rice<ref name="ref1" />.The rice DEP1 (DENSE AND ERECT PANICLE 1) locus was first identified by two independent research groups with quantitative trait loci analysis to control grain yield, grain numbers per panicle, and panicle morphology.Deletion of the DEP1 gene during rice domestication was proposed to enhance meristematic activity and result in reduced inflorescence internode lengths that thereby increased grain numbers per panicle and, consequently, grain yields.''DEP1'' regulates nitrogen uptake and metabolism and participates in determining the amount and direction of cell division,which in turn controls organ size and shape.It has been suggested to encode a plant-specific G protein γ subunit.The DEP1 protein interacts in vivo with both the Gα(RGA1)and Gβ(RGB1)subunits,and reduced RGA1 or enhanced RGB1 activity inhibits nitrogen responses.The plant G protein complex regulates nitrogen signaling and modulation of heterotrimeric G protein activity provides a strategy for environmentally sustainable increases in rice grain yield<ref name="ref2" />.
[[File:cd tolerance.jpg|right|thumb|300px|'''Figure 1.''' ''Impact of the C-terminal half of OsDEP1 on yeast Cd tolerance(from reference<ref name="ref3" />).'']]
*''OsDEP1'' encoded a highly cysteine (Cys)-rich G protein γ subunit composed of 426 aa,which was initially identified as it conferred cadmium (Cd) tolerance on yeast cells. Of the 426 aa constituting OsDEP1, 120 are Cys residues (28.2%), of which 88 are clustered in the C-terminal half region (aa 170-426).The OsDEP1(170–426) region is necessary and sufficient to confer cadmium (Cd)tolerance on host yeast cells(Figure 1).The Cd responses of transgenic Arabidopsis plants constitutively expressing OsDEP1,OsDEP1(1–169) or OsDEP1(170–426),were similar to the observations in yeast cells, with OsDEP1 and OsDEP1(170–426) transgenic plants displaying Cd tolerance but OsDEP1(1–169) plants showing no such tolerance<ref name="ref3" />.Cadmium (Cd) is one of the transition metals that is nonessential for almost all living organisms. It is also a noxious compound that inactivates and denatures structural and functional proteins of organisms by binding to free sulfhydryl groups, thereby inhibiting their growth and development. Another aspect of Cd toxicity is derived from its chemical similarity to metal co-factors or coordinated metals, such as Zn, Fe, and Ca, of enzymes, signalling intermediates, and transcription factors, especially the zinc-finger type.
*Arabidopsis AGG3, a DEP1 homologue, was identified as an Arabidopsis heterotrimeric GTP-binding protein (G protein) γ subunit.Unlike the complex mammalian system, Arabidopsis has only one α (GPA1), one β (AGB1), and three γ (AGG1, AGG2, and AGG3) subunits as components of the heterotrimeric G protein system. OsDEP1 is identified as a cDNA clone that confers Cd tolerance to yeast cells. The gene product, OsDEP1, is highly Cys-rich and is a component of the heterotrimeric G protein signalling pathway.

'''GO assignment(s):''' GO:0005882

*DEP1 (Dense and Erect Panicle1) gene encodes an unknown protein containing the PEBP (phosphatidylethanolamine-binding protein) domain which share some homology with the N terminus of GS3.DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle. In the case of the rice plant, more tillering equates to more grain-bearing branches. Rice branching determines the number of panicle and grain number per panicle ,and then control the grain yield.We can see the rice tillering at (Figure 6).
[[File:The tillering of rice.jpg|right|thumb|300px|'''Figure 6.''' ''The tillering of rice.'']]]]

===Mutation===
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]
*''dep1'' confers an increased number of grains per panicle (and a consequent increase in grain yield).Figure 2 shows the ''DEP1'' and ''dep1'' NIL line field performance.(a) Dense and erect panicle.(b)Increased panicle branching and reduced rachis length. (c)Grain number per main panicle was significantly higher in the presence of ''dep1''<ref name="ref1" />.
[[File:The tillering of rice. .jpg|right|thumb|300px|'''Figure 7.''' ''The tillering of rice(from reference<ref name="ref1" />).'']]
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level(Figure 3)<ref name="ref2" />.
* dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in (Figure 7)<ref name="ref1" />
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]
*DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2<ref name="ref1" />(Fig 8. a).
*But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 8.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 8. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 8. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 8. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.
*The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number<ref name="ref14" /><ref name="ref15" /><ref name="ref16" />. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
*Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 9.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig 9.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 9.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 9.I).The evidence of grain-fillinf failure in the presence of dep1 is unclear.The vascular system of NIL-dep1 plants appeared rather better developed and their sclerenchyma cell walls were thicker at maturity than those in NIL-DEP1 plants. These traits are favorable for both water transport capacity and the mechanical strength of the stem, both of which are important factors for the breeding of high-yielding, lodging-resistant varieties. Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

[[File:DEP1 expression and its effect on cell proliferation.jpg|right|thumb|300px|'''Figure 8.''' ''DEP1 expression and its effect on cell proliferation(from reference<ref name="ref1" />).'']]
[[File:The phenotype of NIL-dep1 plants.jpg|right|thumb|300px|'''Figure 9.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]

===Expression===
[[File:DEP expression2.jpg|right|thumb|300px|'''Figure 4.''' ''The expression profile of DEP1 during spikelet development (from reference<ref name="ref1" />).'']]
*During reproductive development,''DEP1'' was preferentially expressed on the adaxial side of the bract primordium,as well as in the bract primordia of primary and secondary rachis-branches. Within the inflorescence meristem,''DEP1'' was expressed weakly in the carpel and stamen primordia, with patchy expression in the lemma and palea(Figure 4)<ref name="ref1" />.
*Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c)<ref name="ref1" />.
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.

===Cellular Location===
RGB1-GFP, DEP1-GFP,and dep1-1–GFP fusion proteins were detected both on the plasma membrane and within the nucleus of transgenic rice root cells<ref name="ref2" />.

==Evolution==
*Pedigree records show that many high-yielding Chinese japonica varieties, including Shennong 265, were derived from the Italian land race Balilla13,15, which was extensively cultivated in Italy in the 1970s and introduced into China in 1958<ref name="ref8" />.
Genetic diversity analysis suggests that ''DEP1'' has been subjected to artificial selection during ''Oryza sativa'' spp.''japonica'' rice domestication<ref name="ref2" />.
*The allelic constitution at the DEP1 locus was explored by resequencing from a panel of widely cultivated Chinese varieties (69 japonica and 83 indica)<ref name="ref1" />.This truncated mutation was present in Balilla and all 36 japonica types having an erect or semierect panicle, including super high-yielding cultivars Liaojing 5 and Qianchonglang,but it was absent from all the other varieties. Thus, this natural allelic variation in DEP1 has clearly been exploited by japonica breeding programs in China.Several sequence variants at the DEP1 C terminus were present in the sample of indica types. The variety 93-11 differed from the japonica variety Nipponbare by three amino acids, whereas that of the variety Teqing differed by two amino acids. The Nipponbare sequence differed from that of an accession of Oryza rufipogon by one nucleotide at position 663, but this did not produce a variant peptide. We investigated the structure of the homologs of DEP1 in other smallgrain cereals<ref name="ref1" />. Several truncated C-terminal deletions were observed in barley, and in bread wheat and its diploid wild progenitor Triticum urartu. To determine whether any novel gain-of-function was induced by the presence of these truncated genes, we generated a number of transgenic wheat plants carrying a pUbi:RNAi-TaDEP1 construct. The consequent downregulation of TaDEP1 resulted in an increase in the length of the ear, a less compact ear and a somewhat reduced number of spikelets. This suggests that a functionally equivalent mutation may have occurred early in the divergence of the wheat and barley lineages.

==Extension==
[[File:reponses to Cd.jpg|right|thumb|300px|'''Figure 5.''' ''Plant responses to Cd stress (from reference<ref name="ref4" />).'']]
*[http://en.wikipedia.org/wiki/Heterotrimeric_G_proteins Heterotrimeric G proteins] are multisubunit, integral membrane signal-transduction complexes that mediate intracellular responses to external stimuli in diverse eukaryotic organisms<ref name="ref5" />.G proteins typically consist of α, β and γ subunits<ref name="ref6" /><ref name="ref7" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />.
*[http://en.wikipedia.org/wiki/Cadmium Cadmium] (Cd)is one of the transition metals that is non-essential for almost all living organisms.It is also a noxious compound that inactivates and denatures structural and functional proteins of organisms by binding to free sulfhydryl groups,thereby inhibiting their growth and development.Another aspect of Cd toxicity is derived from its chemical similarity to metal co-factors or coordinated metals, such as Zn,Fe,and Ca, of enzymes,signalling intermediates,and transcription factors,especially the zinc-finger type<ref name="ref4" /><ref name="ref11" />. To cope with Cd toxicity effects,plants are known to be equipped with the potential to chelate and extrude Cd,to sequester Cd into vacuoles, and to dissipate reactive oxygen species triggered by Cd(Figure 5)<ref name="ref4" />.For the chelation of heavy metals, including Cd,various cysteine (Cys)-rich proteins are employed by plants.Small Cys-rich peptides,called metallothioneins (MTs),are the major chelators of Cd<ref name="ref12" /><ref name="ref13" />.

Comparison of OsDEP1 and other Cys-rich proteins involved in Cd tolerance:Several other studies have previously identified Cys-rich proteins that can provide enhanced tolerance to Cd toxicity. DcCDT1 from D. ciliaris is a 55 aa peptide of which 15 residues (27%) are Cys. The protein is localized to the cytoplasmic membrane and appears to function in the chelation and possible extrusion of Cd, as transgenic DcCDT1 plants accumulate considerably less Cd than controls.Considering that OsDEP1 is a Gγ subunit, it is likely that it is localized to the inside of cytoplasmic membranes, whereas DcCDT1 may be oriented to the outside of the cytoplasmic membrane. Such a possibility would explain the observed differences in Cd uptake between the DcCDT1- and OsDEP1-expressing transgenic plants.

==Labs working on this gene==
*The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China.
*The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
*The State Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
*Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
*The State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
*Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan.
*National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
*Faculty of Bioresource Sciences, Akita Prefectural University, 241-7 Kaidobata Nishi, Akita 010-1095, Japan.
*Biodiversity and Climate Research Center (BiK-F), D-60323 Frankfurt, Germany.
*The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China.

==References==
<references>
<ref name="ref1">
Huang X, Qian Q, Liu Z, et al. Natural variation at the ''DEP1'' locus enhances grain yield in rice[J]. Nature genetics, 2009, 41(4): 494-497.</ref>
<ref name="ref2">Sun H, Qian Q, Wu K, et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice[J]. Nature genetics, 2014.</ref>
<ref name="ref3"> Kunihiro S, Saito T, Matsuda T, et al. Rice ''DEP1'', encoding a highly cysteine-rich G protein γ subunit, confers cadmium tolerance on yeast cells and plants[J]. Journal of experimental botany, 2013, 64(14): 4517-4527.</ref>
<ref name="ref4">DalCorso G, Farinati S, Maistri S, et al. How plants cope with cadmium: staking all on metabolism and gene expression[J]. Journal of integrative plant biology, 2008, 50(10): 1268-1280.</ref>
<ref name="ref5">New D C, Wong J T Y. The evidence for G-protein-coupled receptors and heterotrimeric G proteins in protozoa and ancestral metazoa[J]. Neurosignals, 1998, 7(2): 98-108.</ref>
<ref name="ref6">Perfus-Barbeoch L, Jones A M, Assmann S M. Plant heterotrimeric G protein function: insights from ''Arabidopsis'' and rice mutants[J]. Current opinion in plant biology, 2004, 7(6): 719-731.</ref>
<ref name="ref7">Jones J C, Duffy J W, Machius M, et al. The crystal structure of a self-activating G protein α subunit reveals its distinct mechanism of signal initiation[J]. Science signaling, 2011, 4(159): ra8.</ref>
<ref name="ref8">Ford C E, Skiba N P, Bae H, et al. Molecular basis for interactions of G protein βγ subunits with effectors[J]. Science, 1998, 280(5367): 1271-1274.</ref>
<ref name="ref9">Ullah H, Chen J G, Young J C, et al. Modulation of cell proliferation by heterotrimeric G protein in ''Arabidopsis''[J]. Science, 2001, 292(5524): 2066-2069.</ref>
<ref name="ref10">Trusov Y, Rookes J E, Tilbrook K, et al. Heterotrimeric G protein γ subunits provide functional selectivity in Gβγ dimer signaling in ''Arabidopsis''[J]. The Plant Cell Online, 2007, 19(4): 1235-1250.</ref>
<ref name="ref11">Verbruggen N, Hermans C, Schat H. Mechanisms to cope with arsenic or cadmium excess in plants[J]. Current opinion in plant biology, 2009, 12(3): 364-372.</ref>
<ref name="ref12"> Ecker D J, Butt T R, Sternberg E J, et al. Yeast metallothionein function in metal ion detoxification[J]. Journal of Biological Chemistry, 1986, 261(36): 16895-16900.</ref>
<ref name="ref13">Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.</ref>
<ref name="ref14">Rao, N.N., Prasad, K., Kumar, P.R. & Vijayraghavan, U. Distinct regulatory role for RFL,the rice LFY homolog, in determining flowering time and plant architecture[J]. Proc. Natl. Acad. Sci. USA 105, 3646–3651 (2008).</ref>
<ref name="ref15">Kellogg, E.A. Floral displays: genetic control of grass inflorescences[J]. Curr. Opin. Plant Biol. 10, 26–31 (2007).</ref>
<ref name="ref16">Kurakawa, T. et al. Direct control of shoot meristem activity by a cytokinin activating enzyme[J]. Nature 445, 652–655 (2007).</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0441900|
Description = Whey acidic protein, core region domain containing protein|
Version = NM_001069822.1 GI:115479386 GeneID:4347178|
Length = 4701 bp|
Definition = Oryza sativa Japonica Group Os09g0441900, 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 9|Chromosome 9]]|
AP = Chromosome 9:17064862..17069562|
CDS = 17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413<br>|
GCID = <gbrowseImage1>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>|
AA = <aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>|
DNA = <dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069822.1 RefSeq:Os09g0441900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

DEP2

2014-06-10T14:30:34Z

Laughin: /* Knowledge extension */

==Annotated Information==
===Function===
*DEP2 gene reduced the development in the longitudinal direction but enhanced the development in the lateral direction of plural organs in rice. In the DEP2 mutants,the panicle length was reduced and panicle diameter was increased<ref name="ref1" />.
*Besides panicle erectness, the DEP2 mutants also showed a slight reduction in plant height , an obvious decrease in panicle length, and a significant increase in both rachis and stem diameter. The leaves of DEP2 are short, wide, and erect, and the overall appearance of the mutant is more compact. The grain density is increased due to the decreased panicle length but not the change of grain number. The grains of the DEP2 mutant are wider and shorter than the wild type<ref name="ref1" />.
*The mutation in DEP2 has pleiotropic effects on plant architecture,and that increased diameter of the rachis and decreased panicle length altogether contributed to the dense and erect panicle phenotype<ref name="ref1" />.
*The DEP2 gene may regulate GA synthesis, and mutation of DEP2 leads to a decrease in plant height<ref name="ref1" />.

[[File:Map-based cloning of the DEP2 gene.png|right|thumb|360px|Map-based cloning of the DEP2 gene(from reference.<ref name="ref1" />.)'']]

===Mutation===
*The DEP2 locus was mapped to the long arm of rice chromosome 7<ref name="ref1" />.
dep2-1:The 31-bp deletion in dep2-1 starts at 2184bp from the initiation codon ATG and caused a frameshift;
dep2-2:the G/A substitution in the second intron of dep2-2 caused an altered splicing site of the second intron and also led to a frameshift.
LOC_Os07g42410 was considered a candidate for the DEP2 gene<ref name="ref1" />.

[[File:DEP2 expression pattern.png|left|thumb|160px|DEP2 expression pattern<ref name="ref1" />'']]

===Expression===
*DEP2 gene expression in the dividing zones of rachis, branches, and florets was higher than in other parts of the rice plant.
*This gene is highly expressed in young panicles ranging from 1 to 15 cm in length;low level expression was also detected in the other organs, including roots,stems,leaves and leaf sheathes.

===Evolution===
*DEP2 may be a plant-specific protein. The only existing low similarity to CIP7 in Arabidopsis is found at the N terminal part of the protein, while the COP1-interacting motif, transcription activation domain, and the nuclear localization signal domain are all missing in DEP2.

===Knowledge extension===
*Except dep2,cl7(t) was a novel allele of dep2. Sequence analysis showed that cl7(t) had a single nucleotide substitution (C to A) in the third exon that leads to a Ser substitution with a stop codon, giving a truncated DEP2 protein.<ref name="ref2" />
*The leaves of the cl7(t) mutant were shorter with a smaller angle between the leaves and stem, and a higher chlorophyll content than that of wild type. Compared with the wild type, the cl7(t) mutant displayed a 30% reduction in panicle length and a marked decrease in the number of grains per panicle. the grains of the mutant were wider and shorter than those of the wild type.<ref name="ref2" />
*The cl7(t) was created by ethyl methanesulfonate mutagenesis.The mutant exhibited cleistogamy,and had closed spikelets, reduced plant height, and altered morphology of the leaves,panicle,and seeds. Further studies demonstrated that the force required to open the lemma and palea was higher in the cl7(t) mutant, and there was weak swelling ability in the lodicules, which leads to cleistogamy.<ref name="ref2" />
*Morphology observation showed no difference between the cl7(t) mutant and wild-type plants from the vegetative developmental stage to the early reproductive stage. However, the cl7(t) mutant exhibited a remarkable phenotype change in terms of flowering. During the heading stage, the wild-type spikelets opened and the anthers protruded outside, whereas the cl7(t) spikelets remained closed. Other than cleistogamy, the architecture of the cl7(t) mutant was also significantly different from that of wild type. The plant height of the cl7(t) mutant was reduced about 20% compared with wild type. The panicles of the cl7(t) mutant remained upright at seed maturity, whereas the panicles of the wild type began to bend as the seed filling caused an increase in grain weight after flowering. The leaves of the cl7(t) mutant were shorter with a smaller angle between the leaves and stem, and a higher chlorophyll content than that of wild type. Its gross plant architecture is similar to the ideal models of japonica rice of Northern China that have high productivity (plant height dwarf, panicle length short, leaf posture erect, leaves wide and short erect panicle.<ref name="ref2" />

==Labs working on this gene==
*Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, PR China
*Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences,Hefei 230031, PR China
*Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei 235000,PR China
*Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, PR China
*College of Life Sciences, Anhui Agricultural University, Hefei 230031, Anhui, PR China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
*Graduate School of the Chinese Academy of Sciences, Beijing 100101, China
*Department of Bioscience,Fukui Prefectural University,4-1-1 Matsuoka Kenjyojima,Eiheiji-cho,Yoshida-gun,Fukui 910-1195,Japan
*Institute of Society for Techno-innovation of Agricuture,Forestry and Fisheries.Tsukuba,Ibaraki 305-0854,Japan
*QTL Genomics Research Center,National Institute of Agrobiological Sciences,Tsukuba,Ibaraki 305-8602,Japan
*Bioscience and Biotechnology Center,Nagoya University,Chikusa,Nagoya 464-8604,Japan
*Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences,Hefei 230031, PR China

===References===
<references>

<ref name="ref1" >Feng Li,Wenbo Liu,Jiuyou Tang,Jinfeng Chen,et al.(2010)Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle out growth and elongation.Cell Research 20:838-849.</ref>
<ref name="ref2" >Da-Hu Ni1,Juan Li,Yong-Bo Duan1,Ya-Chun Yang,Peng-Cheng Wei,Rong-Fang Xu,Chun-Rong Li,Dan-Dan Liang, Hao Li,Feng-Shun Song,Jin-Long Ni,Li Li and Jian-Bo Yang.(2014)Identification and utilization of cleistogamy gene cl7(t) in rice
(Oryza sativa L.).Journal of Experimental Botany, Vol. 65, No. 8, pp. 2107–2117.</ref>