Os05g0158500 - Revision history

192.168.72.52: /* Structured Information */

2015-06-12T07:30:58Z

‎Structured Information

Kristy: /* Location */

2014-06-05T08:55:13Z

‎Location

Kristy: /* References */

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‎References

Kristy: /* Expression */

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‎Expression

Kristy: /* Expression */

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‎Expression

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‎Function

Kristy: /* Function */

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 ===Location===
 Using a double haploid (DH) population (92 lines) derived from a cross between Zhenshan 97 and H94 (both Oryza sativa L. ssp. indica), GS5 was detected in the interval between two molecular markers RM593 and RM574 on the short arm of chromosome 5.
 [[File:GS5 location.jpg]]

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 ==References==
-[1]Lu L, Shao D, Qiu X, et al. Natural variation and artificial selection in four genes determine grain shape in rice[J]. New Phytologist, 2013, 200(4): 1269-1280.
+<references>
-[2]Li Y, Fan C, Xing Y, et al. Natural variation in GS5 plays an important role in regulating grain size and yield in rice[J]. Nature genetics, 2011, 43(12): 1266-1269.
+* <ref name="ref2">
 ==Structured Information==

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 It finds that the levels of GS5 transcript varied drastically among tissues by comparison the temporal and spatial expression pattern of GS5 in two different species, which have different size of grain, using quantitative real-time PCR (qRT-PCR) with total RNA from 14 tissues. Studies also find that the transcript was much more abundant in plants whose grains are wide than those grains are narrow in the palea/lemma at 2, 4 and 5 d before heading, and in the endosperm at 10d after fertilization. These expression differences corresponded well with the critical stages for grain width and grain filling.
-Comparing  genomic  sequences  corresponding to the ORF and the promoter regions of GS5 between varieties with narrow and wide grains. Two varieties with narrow grains (H94 and Minghui 63) had identical sequences, which were very different from the sequence of the wide-grain variety Zhenshan 97. The coding sequences of H94 and Minghui 63 are 1,440 bp in length, encoding a predicted polypeptide of 480 amino acids, whereas the coding sequence of Zhenshan 97 is 1,446 bp, encoding a polypeptide of 482 amino acids. Six bases are inserted 10–15 bp downstream of the translation start site in Zhenshan 97, relative to H94 and Minghui 63, resulting in an in-frame increase of 2 amino acids in the predicted signal peptide. There were also four nucleotide differences in the downstream sequence between the two varietal groups, resulting in substitutions of three amino acids. A comparison of the promoter sequences revealed 18 polymorphisms, including substitutions, deletions and insertions, in one group relative to the other in the 2-kb region upstream of the translation start site. We assayed the temporal and spatial expression patterns of GS5 in NIL(ZS97) and NIL(H94) using quantitative real-time PCR (qRT-PCR) with total RNA from 14 tissues (Supplementary Fig. 3). The levels of GS5 transcript  varied  drastically  among  the  tissues.  In particular, the transcript was much more abundant in NIL(ZS97) than in NIL(H94) in the palea/lemma at 2, 4 and 5 d before heading, and in the endosperm at 10 d after fertilization. Such expression differences corresponded well with the critical stages for grain width and grain filling. Two hypotheses emerged from the comparisons. First, it is possible that the differences in expression levels of GS5are attributable to polymorphisms in the promoter, leading to grain width variation.
+Comparing  genomic  sequences  corresponding to the ORF and the promoter regions of GS5 between varieties with narrow and wide grains. Two varieties with narrow grains (H94 and Minghui 63) had identical sequences, which were very different from the sequence of the wide-grain variety Zhenshan 97. The coding sequences of H94 and Minghui 63 are 1,440 bp in length, encoding a predicted polypeptide of 480 amino acids, whereas the coding sequence of Zhenshan 97 is 1,446 bp, encoding a polypeptide of 482 amino acids. Six bases are inserted 10–15 bp downstream of the translation start site in Zhenshan 97, relative to H94 and Minghui 63, resulting in an in-frame increase of 2 amino acids in the predicted signal peptide. There were also four nucleotide differences in the downstream sequence between the two varietal groups, resulting in substitutions of three amino acids. A comparison of the promoter sequences revealed 18 polymorphisms, including substitutions, deletions and insertions, in one group relative to the other in the 2-kb region upstream of the translation start site. We assayed the temporal and spatial expression patterns of GS5 in NIL(ZS97) and NIL(H94) using quantitative real-time PCR (qRT-PCR) with total RNA from 14 tissues (Fig.4).
 Alternatively, it may be that the grain size differences are attributable to coding variation. We used two approaches to test these hypotheses. First, we sequenced an ~8-kb fragment containing the entire coding region and a 2-kb fragment 5′(upstream) of the translation start site from  the  seven  recombinant  plants  that  we  used  in  fine  mapping (Fig. 1d). Genetic polymorphisms in the promoter region, not the coding region, corresponded well with the phenotypes of the progeny test, which is consistent with the hypothesis that the effect on grain size of GS5is due to variation in the promoter region.

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 ===Expression===
 It finds that the levels of GS5 transcript varied drastically among tissues by comparison the temporal and spatial expression pattern of GS5 in two different species, which have different size of grain, using quantitative real-time PCR (qRT-PCR) with total RNA from 14 tissues. Studies also find that the transcript was much more abundant in plants whose grains are wide than those grains are narrow in the palea/lemma at 2, 4 and 5 d before heading, and in the endosperm at 10d after fertilization. These expression differences corresponded well with the critical stages for grain width and grain filling.
 ===Location===

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 The quantitative trait locus (QTL) GS5 in rice controls	grain size by regulating grain width, filling and weight. GS5 encodes a	putative serine arboxypeptidase,which belongs to the peptidase S10 family， and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51	rice accessions	from a wide geographic range identified three haplotypes that seem to be associated with grain	width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield	in rice	and, potentially,other crops.<ref name="ref2" />
-It also functions putatively as a positive modulator upstream of cell cycle genes, and its overexpression can result in an increase in cell numbers by promoting mitotic division. Besides,it can increase cell size to some extent leading to enhanced latitudinal growth in the grain.
+It also functions putatively as a positive modulator upstream of cell cycle genes, and its overexpression can result in an increase in cell numbers by promoting mitotic division. Besides,it can increase cell size to some extent leading to enhanced latitudinal growth in the grain.<ref name="ref1" />
 The effects of GS5 on grain size and filling.（Fig.1）

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 [[File:Effects.jpg]]
-The effect of GS5on cell number and size in lemma/palea. （Fig.2）
+The effect of GS5 on cell number and size in lemma/palea. （Fig.2）
 [[File:effect2.jpg]]
-Regulation by GS5of the expression of genes involved in the cell cycle.（Fig.3）
+Regulation by GS5 of the expression of genes involved in the cell cycle.（Fig.3）
 [[File:effect3.jpg]]

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 This is a minor QTL for GW,also known as GS5. Forty-one SNPs and six InDels were detected in the 6.4-kb genomic region of GS5. Of these, 34 SNPs and three InDels were located in the promoter; two InDels were detected in the ﬁrst exon, resulting in a change of two to ﬁve Glys. Three contiguous SNPs were located in the second exon, leading to two amino acid changes; a nonsynonymous SNP was detected in the ninth exon, and the remaining six SNPs were located in an intron and the 3’UTR.
 ===Function===
-The quantitative trait locus (QTL) GS5 in rice controls	grain size by regulating grain width, filling and weight. GS5 encodes a	putative serine arboxypeptidase,which belongs to the peptidase S10 family， and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51	rice accessions	from a wide geographic range identified three haplotypes that seem to be associated with grain	width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield	in rice	and, potentially,other crops.<ref name="ref1" />
+The quantitative trait locus (QTL) GS5 in rice controls	grain size by regulating grain width, filling and weight. GS5 encodes a	putative serine arboxypeptidase,which belongs to the peptidase S10 family， and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51	rice accessions	from a wide geographic range identified three haplotypes that seem to be associated with grain	width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield	in rice	and, potentially,other crops.<ref name="ref2" />
 It also functions putatively as a positive modulator upstream of cell cycle genes, and its overexpression can result in an increase in cell numbers by promoting mitotic division. Besides,it can increase cell size to some extent leading to enhanced latitudinal growth in the grain.