RiceWiki - User contributions [en]

Qsw5

2014-06-07T14:51:24Z

Zhaoyanyan:

Function
The biological function of gene Qsw5 is that it through increasing the number of cells in rice flowers lemma,then increaseing the capacity of rice husk, and ultimately increase the grain width.Pets the gene loci of Kasalath qSW5, the grain width lines into smaller, field production decreased by 10%.But through the gene RNAi regulate ORF1's expression down (ORF1 is one sets of Kasalath qSW5) ,then can make larger grain width and increase output.Therefore, loss of function qSW5 sites have value in breeding.

Expression
Qsw5 can be involved in the expression of rice seed colors .
Variation in the colors of the rice seed pericarp of the previous ‘heritage landraces’. These landraces retain all functional alleles of three domestication-related genes (qSW5, Wx and qSH1) at the three FNP positions (Shomura et al. 2008).
Use japonica rice Nipponbare with indica rice Kasalath hybrid to biuld F2 population,In the fifth chromosome location to a control grain width of main effect QTL, it ie the Qsw5.Through positional cloning puting qSW5 finly positioning into 2263 bp, Finally,through gene expression analysis, and a complementary experiment to determine which one ORF (open reading frame) of qSW5.
Qsw5 can be involved in the expression of rice seed width.
Evolution
By combining qSW5, wx and qSH1 variation of these three genes form the current "Nipponbare."
Rice seed size is an important agronomic trait in determining the yield potential, and four seed size related genes (GS3, GW2, qSW5/GW5 and GIF1) have been cloned in rice so far. However, the relationship among these four genes is still unclear, which will impede the process of gene pyramiding breeding program to some extent. To shade light on the relationship of above four genes, gene expression analysis was performed with GS3-RNAi, GW2-RNAi lines and CSSL of qSW5 at the transcriptional level. The results clearly showed that qSW5 and GW2 positively regulate the expression of GS3. Meanwhile, qSW5 can be down-regulated by repression of GW2 transcription. Additionally, GIF1 expression was found to be positively regulated by qSW5 but negatively by GW2 and GS3. Moreover, the allelic effects of qSW5 and GS3 were detailedly characterized based on a natural population consisting of 180 rice cultivars. It was indicated that mutual interactions exist between the two genes, in which, qSW5 affecting seed length is masked by GS3 alleles, and GS3 affecting seed width is masked by qSW5 alleles. These findings provide more insights into the molecular mechanisms underlying seed size development in rice and are likely to be useful for improving rice grain yield.
[1]. Alonso-Blanco C, Aarts MG, Bentsink L, Keurentjes JJ, Reymond M, Vreugdenhil D, et al. What has natural variation taught us about plant development, physiology, and adaptation?[J]. The Plant cell. 2009,21(7):1877-96.
[2]. Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I, et al. A novel kinesin 13 protein regulating rice seed length[J]. Plant & cell physiology. 2010,51(8):1315-29.
[3]. Konishi S, Ebana K, Izawa T. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars[J]. Plant & cell physiology. 2008,49(9):1283-93.
[4]. Tanabata T, Shibaya T, Hori K, Ebana K, Yano M. SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis[J]. Plant physiology. 2012,160(4):1871-80.

Qsw5

2014-06-06T06:47:56Z

Zhaoyanyan:

Function
The biological function of gene Qsw5 is that it through increasing the number of cells in rice flowers lemma,then increaseing the capacity of rice husk, and ultimately increase the grain width.Pets the gene loci of Kasalath qSW5, the grain width lines into smaller, field production decreased by 10%.But through the gene RNAi regulate ORF1's expression down (ORF1 is one sets of Kasalath qSW5) ,then can make larger grain width and increase output.Therefore, loss of function qSW5 sites have value in breeding.

Expression
Qsw5 can be involved in the expression of rice seed colors .
Variation in the colors of the rice seed pericarp of the previous ‘heritage landraces’. These landraces retain all functional alleles of three domestication-related genes (qSW5, Wx and qSH1) at the three FNP positions (Shomura et al. 2008).
Use japonica rice Nipponbare with indica rice Kasalath hybrid to biuld F2 population,In the fifth chromosome location to a control grain width of main effect QTL, it ie the Qsw5.Through positional cloning puting qSW5 finly positioning into 2263 bp, Finally,through gene expression analysis, and a complementary experiment to determine which one ORF (open reading frame) of qSW5.
Qsw5 can be involved in the expression of rice seed width.
Evolution
By combining qSW5, wx and qSH1 variation of these three genes form the current "Nipponbare."
Genome dynamics for qSW5, Rc and Wx mutations during rice domestication. (A) Geographical origins of the rice cultivars used in this analysis. Six groups (indicated by different colors) are shown. (B) Selected heatmaps of the genomic relationships from the 91 tested japonica rice cultivars (Supplementary Fig. S1), based on the increase in the occurrence of defects in three FNPs of three domesticationrelated genes: qSW5, Rc and Wx. Here, only cultivars with all of the functional Rd1, Rd2 and qSH1 alleles were picked up. In each genotype, upper case letters indicate the functional allele and lower case letters indicate the non-functional allele (colored red). Local origins of each landrace are indicated by colored bars, which correspond to the colors in (A). In the FNP patterns, yellow indicates the functional allele and red indicates the non-functional allele. The heatmap was constructed on the basis of the pairwise genome distance
calculated from the RFLP patterns. Colors in the heatmap indicate genome distances from the other cultivars. Each line of the heatmap indicates a specified cultivar with the six FNP genotype among the 91 lines. The yellow box in the heatmap indicates the position for the cultivar of the line among the 91 row cultivars. Each row indicates the genome distance, indicated by colors, to the corresponding cultivar. The order of the top row cultivars was determined by similarity clusters of genome RFLP patterns. The colors at the top correspond here to the local origins.
[1]. Alonso-Blanco C, Aarts MG, Bentsink L, Keurentjes JJ, Reymond M, Vreugdenhil D, et al. What has natural variation taught us about plant development, physiology, and adaptation?[J]. The Plant cell. 2009,21(7):1877-96.
[2]. Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I, et al. A novel kinesin 13 protein regulating rice seed length[J]. Plant & cell physiology. 2010,51(8):1315-29.
[3]. Konishi S, Ebana K, Izawa T. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars[J]. Plant & cell physiology. 2008,49(9):1283-93.
[4]. Tanabata T, Shibaya T, Hori K, Ebana K, Yano M. SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis[J]. Plant physiology. 2012,160(4):1871-80.

Qsw5

2014-06-06T04:26:20Z

Zhaoyanyan:

Function
The biological function of gene Qsw5 is that it through increasing the number of cells in rice flowers lemma,then increaseing the capacity of rice husk, and ultimately increase the grain width.Pets the gene loci of Kasalath qSW5, the grain width lines into smaller, field production decreased by 10%.But through the gene RNAi regulate ORF1's expression down (ORF1 is one sets of Kasalath qSW5) ,then can make larger grain width and increase output.Therefore, loss of function qSW5 sites have value in breeding.

Expression
As Darwin (1857) noted, crop domestication resembles a rapid evolutionary process that results from artificial selection but that otherwise has all the characteristics of evolution by means of natural selection. With increasing availability of crop genome information, the accumulation of knowledge about domestication-related genes, and the identification of functional nucleotide polymorphisms (FNPs), the crop domestication process is being increasingly elucidated (Doebley et al. 2006). In maize, for example, extensive genome analysis to find genes with reduced natural variation among cultivars, landraces and their wild relatives has suggested that thousands of genes might have been subjected to selection during domestication (Gaut et al. 2000, Matsuoka et al. 2002, Yamasaki et al. 2005). In wheat, archeological analysis of plant remains has revealed that the domestication process took a few thousand years (Tanno and Willcox 2006, Dubcovsky and Dvorak 2007). In barley, natural variation among landraces from Europe to Asia has been examined to reveal how barley cultivation propagated throughout these regions, with some genome changes detected and two distinct domestication processes proposed for European and Asian barley (Morrell and Clegg 2007, Pourkheirandish and Komatsuda 2007, Saisho and Purugganan 2007). In addition, some domestication-related genes have been cloned, and key natural variations in these genes (i.e. FNPs) have been examined to elucidate the domestication process in several crops, including maize, wheat and barley (Wang et al. 2005, Doebley et al. 2006, Simons et al. 2006, Komatsuda et al. 2007), even though the domestication process itself remains largely unknown.
Evolution
We can express the OsSUT gene in yeast to test whether it's functional. Choose the yeast strain which is unable to hydrolyse exogenous sucrose but if transformed with a functional SUT, can import sucrose and hydrolyse it internally , allowing it to grow on media containing sucrose as the sole carbon source.

" Test function in yeast(from reference [2]).. "
There is also a novel fluorescent assay for sucrose transporter activity based on the ability of type I SUTs to transport the highly fluorescent molecule esculin (6,7-dihydroxycoumarin β-D-glucoside). Using fluorescence microscopy, we can do the research conveniently.

" Esculin uptake by yeast cells expressing StSUT1 was detected using FACS.(from reference [5]).. "Labs working on this gene

Univ Minnesota, Dept Plant Biol, Biol Sci Ctr 250, 1445 Gortner Ave, St Paul, MN 55108 USA.
CSIRO Plant Ind, Canberra, ACT 2601, Australia.
Chinese Acad Sci, Inst Genet & Dev Biol, Natl Key Lab Plant Genom, Beijing 100101, Peoples R China
Natl Agr Res Ctr, Dept Rice Res, Niigata 9430193, Japan
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences,Peoples R China
Department of Rice Research, National Agricultural Research Center, Joetsu, Niigata, 943-0193 JapanReferences

↑ Lu J M-Y. and Bush D R.(1998) His-65 in the proton-sucrose symporter is an essential amino acid whose modification with site-directed mutagenesis increases transport activity. Proc Natl Acad 95: 9025–9030.
↑ 2.0 2.1 2.2 Aoki N, Hirose T, Scofield G N, et al.(2003）The Sucrose Transporter Gene Family in Rice. Plant and Cell Physiology 44:223-232.
↑ Furbank R T, Scofield G N, Hirose T, et al. (2001) Cellular localisation and function of a sucrose transporter OsSUT1 in developing rice grains. Aust. J. Plant Physiol 28: 1187–1196.
↑ Hirose T, Imaizumi N, Scofield G N, et al. (1997) cDNA cloning and tissue-specific expression of a gene for sucrose transporter from rice (Oryza sativa L.). Plant Cell Physiol 38: 1389–1396.
↑ Gora P J, Reinders A, Ward J M, et al.(2012)A novel fluorescent assay for sucrose transporters. Plant Methods 8:13.

Qsw5

2014-06-06T03:20:57Z

Zhaoyanyan:

Function
The biological function of gene Qsw5 is that it through increasing the number of cells in rice flowers lemma,then increaseing the capacity of rice husk, and ultimately increase the grain width.Pets the gene loci of Kasalath qSW5, the grain width lines into smaller, field production decreased by 10%.But through the gene RNAi regulate ORF1's expression down (ORF1 is one sets of Kasalath qSW5) ,then can make larger grain width and increase output.Therefore, loss of function qSW5 sites have value in breeding.

The five families of sucrose transporters involve in the rice resistance to intermittent drought and secondary soil salinity.
OsSUT1 is the major salt responsive gene of the family of 5 OsSUT-genes，The function of the rice OsSUT1-gene in carbon partitioning, specifically for grain filling and seed germination and early seedling growth.OsSUT1 plays in the transport of assimilate along the entire long-distance pathway, from the flag leaf blade to the base of the filling grain.
Expression
The five families all contained a region that is highly conserved in known functional plant SUT genes, including OsSUT1. This domain includes the first membrane spanning helix, the following extracellular loop, the second membrane spanning helix and the next cytoplasmic loop have shown, by site-directed mutagenesis of the Arabidopsis AtSUC1 protein, that a conserved histidine residue in the extracellular loop is responsible for sucrose binding in the transport process. This histidine residue was also found to be present in all of the putative OsSUT peptides(reference [1] ). .

" The functionally important and conserved histidine residue is shown in bold. Dots indicate non-conserved amino acids, and horizontal bars indicate gaps in the sequence alignments(from reference [2]).. "

OsSUT1 mRNA accumulated to high levels in germinating seeds, source leaf sheaths and panicles, but to very low level in roots. OsSUT2 mRNA accumulated to nearly equal levels in all tissues tested. The expression patterns of OsSUT3 and 5 were found to be similar, the expression level is at its highest in sink leaves and the lowest in germinating seeds. OsSUT4 showed preferential expression in sink leaves(reference [3] and reference [4]).

" Analysis of expression of the five OsSUT genes, by semi-quantitative RT-PCR. For each gene, transcript levels in different tissue samples are comparable(from reference [2]).. "
The gene expression are different when the plants encounter such environmental obstacles, although the five families involved in the sucrose transporters and sucrose transport, they expressed differently in different tissues.OsSUT1 expression appeared to be non-essential for vegetative growth. Performance of OsSUT1 anti-sense lines in response to increasing salt concentrations.
Evolution
We can express the OsSUT gene in yeast to test whether it's functional. Choose the yeast strain which is unable to hydrolyse exogenous sucrose but if transformed with a functional SUT, can import sucrose and hydrolyse it internally , allowing it to grow on media containing sucrose as the sole carbon source.

" Test function in yeast(from reference [2]).. "
There is also a novel fluorescent assay for sucrose transporter activity based on the ability of type I SUTs to transport the highly fluorescent molecule esculin (6,7-dihydroxycoumarin β-D-glucoside). Using fluorescence microscopy, we can do the research conveniently.

" Esculin uptake by yeast cells expressing StSUT1 was detected using FACS.(from reference [5]).. "Labs working on this gene

Univ Minnesota, Dept Plant Biol, Biol Sci Ctr 250, 1445 Gortner Ave, St Paul, MN 55108 USA.
CSIRO Plant Ind, Canberra, ACT 2601, Australia.
Chinese Acad Sci, Inst Genet & Dev Biol, Natl Key Lab Plant Genom, Beijing 100101, Peoples R China
Natl Agr Res Ctr, Dept Rice Res, Niigata 9430193, Japan
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences,Peoples R China
Department of Rice Research, National Agricultural Research Center, Joetsu, Niigata, 943-0193 JapanReferences

↑ Lu J M-Y. and Bush D R.(1998) His-65 in the proton-sucrose symporter is an essential amino acid whose modification with site-directed mutagenesis increases transport activity. Proc Natl Acad 95: 9025–9030.
↑ 2.0 2.1 2.2 Aoki N, Hirose T, Scofield G N, et al.(2003）The Sucrose Transporter Gene Family in Rice. Plant and Cell Physiology 44:223-232.
↑ Furbank R T, Scofield G N, Hirose T, et al. (2001) Cellular localisation and function of a sucrose transporter OsSUT1 in developing rice grains. Aust. J. Plant Physiol 28: 1187–1196.
↑ Hirose T, Imaizumi N, Scofield G N, et al. (1997) cDNA cloning and tissue-specific expression of a gene for sucrose transporter from rice (Oryza sativa L.). Plant Cell Physiol 38: 1389–1396.
↑ Gora P J, Reinders A, Ward J M, et al.(2012)A novel fluorescent assay for sucrose transporters. Plant Methods 8:13.

Qsw5

2014-06-05T15:48:56Z

Zhaoyanyan: Created page with "Function Plant sucrose transporters (SUTs) regulate the active transport of sucrose across plasma membrane barriers in a process that is coupled to proton symport. Since sucro..."

Function
Plant sucrose transporters (SUTs) regulate the active transport of sucrose across plasma membrane barriers in a process that is coupled to proton symport. Since sucrose is the major carbohydrate translocated through the phloem in most plant species, the sucrose/H+ symporters are thought to play important roles in mediating carbon partitioning in plants, for example apoplastic phloem loading in leaves, transport of sucrose into and/or out of temporary storage sinks such as stem tissue and post-phloem transport of sucrose into sink tissue such as seeds.
The rice has five families of sucrose transporters. Despite of the previously reported OsSUT1, four putative sucrose transporter are known as OsSUT2, 3, 4 and 5. OsSUT1 encodes a functional SUT protein that is essential for transport of assimilate into filling rice grains. It has also been proposed that OsSUT1 is involved in transport of assimilate remobilised from starch reserves in leaf sheaths and in germinating seeds. Expression of OsSUT3, 4 and 5 in sink rice leaf suggests that they may be important for supplying sucrose, as a carbon source for growing tissues or possibly to supply sucrose to temporary storage tissues.Unlike the other four OsSUT genes, OsSUT2 seems to be expressed at almost equal levels in various tissues of rice plants.
The five families of sucrose transporters involve in the rice resistance to intermittent drought and secondary soil salinity.
OsSUT1 is the major salt responsive gene of the family of 5 OsSUT-genes，The function of the rice OsSUT1-gene in carbon partitioning, specifically for grain filling and seed germination and early seedling growth.OsSUT1 plays in the transport of assimilate along the entire long-distance pathway, from the flag leaf blade to the base of the filling grain.
Expression
The five families all contained a region that is highly conserved in known functional plant SUT genes, including OsSUT1. This domain includes the first membrane spanning helix, the following extracellular loop, the second membrane spanning helix and the next cytoplasmic loop have shown, by site-directed mutagenesis of the Arabidopsis AtSUC1 protein, that a conserved histidine residue in the extracellular loop is responsible for sucrose binding in the transport process. This histidine residue was also found to be present in all of the putative OsSUT peptides(reference [1] ). .

" The functionally important and conserved histidine residue is shown in bold. Dots indicate non-conserved amino acids, and horizontal bars indicate gaps in the sequence alignments(from reference [2]).. "

OsSUT1 mRNA accumulated to high levels in germinating seeds, source leaf sheaths and panicles, but to very low level in roots. OsSUT2 mRNA accumulated to nearly equal levels in all tissues tested. The expression patterns of OsSUT3 and 5 were found to be similar, the expression level is at its highest in sink leaves and the lowest in germinating seeds. OsSUT4 showed preferential expression in sink leaves(reference [3] and reference [4]).

" Analysis of expression of the five OsSUT genes, by semi-quantitative RT-PCR. For each gene, transcript levels in different tissue samples are comparable(from reference [2]).. "
The gene expression are different when the plants encounter such environmental obstacles, although the five families involved in the sucrose transporters and sucrose transport, they expressed differently in different tissues.OsSUT1 expression appeared to be non-essential for vegetative growth. Performance of OsSUT1 anti-sense lines in response to increasing salt concentrations.
Evolution
We can express the OsSUT gene in yeast to test whether it's functional. Choose the yeast strain which is unable to hydrolyse exogenous sucrose but if transformed with a functional SUT, can import sucrose and hydrolyse it internally , allowing it to grow on media containing sucrose as the sole carbon source.

" Test function in yeast(from reference [2]).. "
There is also a novel fluorescent assay for sucrose transporter activity based on the ability of type I SUTs to transport the highly fluorescent molecule esculin (6,7-dihydroxycoumarin β-D-glucoside). Using fluorescence microscopy, we can do the research conveniently.

" Esculin uptake by yeast cells expressing StSUT1 was detected using FACS.(from reference [5]).. "Labs working on this gene

Univ Minnesota, Dept Plant Biol, Biol Sci Ctr 250, 1445 Gortner Ave, St Paul, MN 55108 USA.
CSIRO Plant Ind, Canberra, ACT 2601, Australia.
Chinese Acad Sci, Inst Genet & Dev Biol, Natl Key Lab Plant Genom, Beijing 100101, Peoples R China
Natl Agr Res Ctr, Dept Rice Res, Niigata 9430193, Japan
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences,Peoples R China
Department of Rice Research, National Agricultural Research Center, Joetsu, Niigata, 943-0193 JapanReferences

↑ Lu J M-Y. and Bush D R.(1998) His-65 in the proton-sucrose symporter is an essential amino acid whose modification with site-directed mutagenesis increases transport activity. Proc Natl Acad 95: 9025–9030.
↑ 2.0 2.1 2.2 Aoki N, Hirose T, Scofield G N, et al.(2003）The Sucrose Transporter Gene Family in Rice. Plant and Cell Physiology 44:223-232.
↑ Furbank R T, Scofield G N, Hirose T, et al. (2001) Cellular localisation and function of a sucrose transporter OsSUT1 in developing rice grains. Aust. J. Plant Physiol 28: 1187–1196.
↑ Hirose T, Imaizumi N, Scofield G N, et al. (1997) cDNA cloning and tissue-specific expression of a gene for sucrose transporter from rice (Oryza sativa L.). Plant Cell Physiol 38: 1389–1396.
↑ Gora P J, Reinders A, Ward J M, et al.(2012)A novel fluorescent assay for sucrose transporters. Plant Methods 8:13.