Differential expression of GS5 regulates grain size in rice

Xu, Chunjue; Yu, Liu; Li, Yibo; Xu, Xiaodong; Xu, Caiguo; Li, Xianghua; Xiao, Jinghua; Zhang, Qifa

doi:10.1093/jxb/erv058

Cited by 133 publications

(83 citation statements)

References 41 publications

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“…Another QTL for grain size, GS5, with a minor effect on grain width, was annotated as collinear between ZS97 and MH63, as the causal mutation was two SNPs in the promoter region with little alteration in their CDSs (25,26). Genetic analyses showed that all these genes contribute complementary effects to the performance of the F 1 hybrid (23)(24)(25)(26). A similar situation can also be found with a number of disease-resistance genes (27,28).…”

Section: Resultsmentioning

confidence: 83%

“…More specifically, three genes for yield traits were cloned based on populations derived from a ZS97/MH63 cross (23)(24)(25)(26). For example, Ghd7, a gene having large effects simultaneously on the number of grains, plant height, and heading date (23), belongs to the PAV category, located in a presence fragment (MH07p00800) in MH63 but absent in ZS97 (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The mutant MH63 allele produces long grains, whereas the wild-type ZS97 allele results in a short grain phenotype (24). Another QTL for grain size, GS5, with a minor effect on grain width, was annotated as collinear between ZS97 and MH63, as the causal mutation was two SNPs in the promoter region with little alteration in their CDSs (25,26). Genetic analyses showed that all these genes contribute complementary effects to the performance of the F 1 hybrid (23)(24)(25)(26).…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Zhang

Chen

Feng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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212

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Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.Oryza sativa | reference genomes | BAC-by-BAC strategy | transcriptome R ice is one of the most important food crops in the world and provides more than 20% of the caloric intake for one-half of the world's population. Asian cultivated rice can be divided into two subspecies-that is, Oryza sativa subsp. indica and O. sativa subsp. japonica-which are highly distinctive in geographical distribution, reproductively isolated, and have been shown to have extensive differentiation in genome structure and gene content (1). Indica rice accounts for more than 70% of world rice production (2) and is genetically much more diverse than japonica rice (3). Genomic studies have established that indica rice can be further subdivided into two major varietal groups, indica I and indica II, which have been independently bred and widely cultivated in China and Southeast Asia, respectively (4). Hybrids between these groups usually show strong heterosis, which provided the basis for the great success of hybrid rice in several countries, including China and the United States. For example, Zhenshan 97 (ZS97, indica I) and Minghui 63 (MH63, indica II) are the parents of the elite hybrid Shanyou 63 (SY63) (SI Appendix, Fig. S1 A and B), which exhibits superiority for a large array of agronomic traits including yield, resistance to multiple diseases, wide adaptability, and good eating quality, and thus has been the most widely cultivated hybrid in China over the past three decades (SI Appendix, Fig. S1C).Because of the importance of hybrid rice in helping to ensure a stable and secure food supply for generations, a series of attempts have been...

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Section: Resultsmentioning

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Zhang

Chen

Feng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

212

228

View full text Add to dashboard Cite

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“…Comparison with other sequences encoding rice BAK1, somatic embryo receptor kinase (SERK) or SERK-like (SERL) (Singla et al, 2009;Park et al, 2011;Xu et al, 2015) demonstrated that OsI-BAK1 is lack of a complete kinase domain, serine proline-rich domain and C-terminal domain (Fig. 1A).…”

Section: Sequence Analysis and Transcript Profiling Of Osi-bak1mentioning

confidence: 99%

Brassinosteroid insensitive 1-associated kinase 1 (OsI-BAK1) is associated with grain filling and leaf development in rice

Khew

Teo

Chan

et al. 2015

Journal of Plant Physiology

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“…In recent years, substantial research progress has been made regarding genes associated with grain size, particularly research focused on GS3, qSW5, GW2, GS3, GS5, and TGW6 haplotypes (Weng et al, 2008;Fan et al, 2009;Takano-Kai et al, 2009;Mao et al, 2010;Li et al, 2011;Dixit et al, 2013;Ishimaru et al, 2013;Lu et al, 2013;Xu et al, 2015). Zhang et al (2012) found that only SNP1 in the qGL3 region in 94 germplasms (the same SNP that was found in TD70) contributed highly to grain length, whereas other polymorphic sites had no significant contributions to grain length.…”

Section: Haplotypes Of Genes Associated With Grain Sizementioning

confidence: 99%

Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice

Zhang¹,

Zhu²,

QingYong³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Grain size is an important trait that directly influences rice yield. The qGL3 and GS3 genes are two putative regulators that play a role in grain size determination. A single rare nucleotide substitution (C→A) at position 1092 in exon 10 of qGL3 might be responsible for variations in grain size. However, little is known about the haplotype variations of qGL3 and their interactions with GS3 during the regulation of grain length and grain weight. In this study, qGL3 haplotype variations were examined in 61 Indica varieties, and the effects of qGL3 and GS3 on grain trait variation in 110 lines were evaluated. Six qGL3 haplotypes were identified, and qGL3-2 was a major haplotype in Indica varieties. Moreover, qGL3-6, a reported key single nucleotide polymorphism, was validated. Our results showed that the mutants qgl3 and gs3 (loss-of-function mutation types of qGL3 and GS3, respectively) had significant effects on grain length and grain weight. However, no significant effects associated with differences in the regulation of grain thickness were observed. The genetic effects of qgl3 on grain phenotypes were stronger than those of gs3. In addition to increased grain length, qgl3 had an evident role in grain width increases. In contrast, gs3 played an opposite role in grain width regulation. These results provided novel insights into grain size control and the functions of qgl3 and gs3 in rice yield improvement.

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Differential expression of GS5 regulates grain size in rice

Abstract: HighlightTwo SNPs in the promoter of GS5 are responsible for expression variation controlling grain size. Enhanced expression of GS5 competitively inhibits the interaction between OsBAK1 and OsMSBP1, promoting grain size.

Cited by 133 publications

References 41 publications

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Brassinosteroid insensitive 1-associated kinase 1 (OsI-BAK1) is associated with grain filling and leaf development in rice

Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice

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