Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice
Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice
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水稻籽粒形状相关性状的全基因组关联分析和等位基因挖掘
DOI：
10.1016/j.rsci.2018.09.002
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发表时间：
2019-11-01
期刊：
影响因子：
4.8
通讯作者：
Guo Longbiao
中科院分区：
文献类型：
--
作者：
Lv Yang;Wang Yueying;Guo Longbiao
挖掘与水稻粒形显著相关的单核苷酸多态性（SNPs），通过全基因组关联分析（GWAS）预测候选基因，可为水稻优良遗传资源的发现和利用提供理论依据。以161份不同粒型的南方籼稻品种为材料，基于16 352个SNPs，对粒长、粒宽、千粒重和粒长/粒宽4个粒形相关性状进行遗传变异分析。表型统计结果表明，这4个性状的变异系数分别为9.92%、9.09%、20.20%和16.38%。各性状均呈正态分布，且性状间存在一定的相关性。通过一般线性模型相关分析，共鉴定出38个显著位点，并将显著位点上下游100 kb范围确定为候选区间。在3号染色体上，发现GS 3和qGL 3调节GL。在6号染色体上，发现TGW 6和GW 6a调节TGW。在第5和第9染色体上也发现了与粒形相关的QTL。此外，利用已测序的3 K-种质资源，我们发现这两个自然群体之间有22个重叠品种。在GS 3基因的5个区域共检测到26个SNPs和14种单倍型。候选区间内多个候选基因/QTL的检测有利于进一步挖掘水稻上级遗传资源。
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.