Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

文献类型： 外文期刊

第一作者： Lv Yang

作者： Lv Yang;Wang Yueying;Jahan, Noushin;Hu Haitao;Chen Ping;Shang Lianguang;Lin Haiyan;Dong Guojun;Hu Jiang;Gao Zhenyu;Qian Qian;Zhang Yu;Guo Longbiao;Zhang Yu

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关键词： candidate gene; grain shape; genome-wide association study; haplotype; rice; single nucleotide polymorphism

期刊名称：RICE SCIENCE （ 影响因子：3.333； 五年影响因子：4.226 ）

ISSN： 1672-6308

年卷期： 2019 年 26 卷 6 期

页码：

收录情况： SCI

摘要： Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.

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