Candidate gene analysis of rice grain shape based on genome-wide association study.

IF 4.4 1区 农林科学 Q1 AGRONOMY
Wei Xin, Ning Chen, Jiaqi Wang, Yilei Liu, Yifeng Sun, Baojia Han, Xinghua Wang, Zijie Liu, Hualong Liu, Hongliang Zheng, Luomiao Yang, Detang Zou, Jingguo Wang
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引用次数: 0

Abstract

Key message: Thirteen QTLs associated with rice grain shape were localized by genome-wide association study. LOC_Os01g74020, the putative candidate gene in the co-localized QTL-qGSE1.2 interval, was identified and validated. Grain shape (GS) is a key trait that affects yield and quality of rice. Identifying and analyzing GS-related genes and elucidating the physiological, biochemical and molecular mechanisms are important for rice breeding. In this study, genome-wide association studies (GWAS) were conducted based on 1, 795, 076 single-nucleotide polymorphisms (SNPs) and three GS-related traits, grain length (GL), grain width (GW) and thousand-grain weight (TGW), in a natural population which comprised 374 rice varieties. A total of 13 quantitative trait locus (QTLs) related to GL, GW and TGW were identified, respectively, of which two QTLs (qGSE1.2 and qGSE5.3) were associated with both GL and TGW. A known key GS regulatory gene, GW5, was present in the interval of qGSE5.3. Based on the qRT-PCR results, LOC_Os01g74020 (OsGSE1.2) was identified as a GS candidate gene. Functional analysis of OsGSE1.2 showed that glume cell width and GW were significantly reduced, and that glume cell length, GL, TGW and single-plant yield were significantly increased in OsGSE1.2 knockout lines than those of wild type. OsGSE1.2 affects rice grain length by suppressing the elongation of glume cell and is a novel GS regulatory gene. These findings laid the foundation for molecular breeding to improve rice GS and increase rice yield and profitability.

基于全基因组关联研究的水稻粒形候选基因分析
关键信息:通过全基因组关联研究定位了13个与水稻粒形相关的QTL。鉴定并验证了共定位 QTL-qGSE1.2 区间的推测候选基因 LOC_Os01g74020。粒形(GS)是影响水稻产量和品质的关键性状。鉴定和分析GS相关基因并阐明其生理、生化和分子机制对水稻育种非常重要。本研究在一个由 374 个水稻品种组成的自然群体中,基于 1,795,076 个单核苷酸多态性(SNPs)和三个 GS 相关性状(粒长(GL)、粒宽(GW)和千粒重(TGW))进行了全基因组关联研究(GWAS)。共鉴定出 13 个与 GL、GW 和 TGW 相关的数量性状位点(QTL),其中两个 QTL(qGSE1.2 和 qGSE5.3)与 GL 和 TGW 均相关。在 qGSE5.3 的区间内有一个已知的 GS 关键调控基因 GW5。根据 qRT-PCR 结果,LOC_Os01g74020(OsGSE1.2)被确定为 GS 候选基因。对 OsGSE1.2 的功能分析表明,与野生型相比,OsGSE1.2 基因敲除株的颖壳宽度和 GW 显著减少,而颖壳长度、GL、TGW 和单株产量显著增加。OsGSE1.2通过抑制颖壳细胞的伸长来影响水稻谷粒的长度,是一个新的GS调控基因。这些发现为分子育种改良水稻GS、提高水稻产量和收益奠定了基础。
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来源期刊
CiteScore
9.60
自引率
7.40%
发文量
241
审稿时长
2.3 months
期刊介绍: Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.
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