A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection
A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection
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DOI：
10.3835/plantgenome2015.04.0024
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发表时间：
2015-11-01
期刊：
影响因子：
4.2
通讯作者：
Lorenz, Aaron
中科院分区：
文献类型：
--
作者：
Bandillo, Nonoy;Jarquin, Diego;Lorenz, Aaron
对作物种质资源进行的群体结构分析和全基因组关联研究（GWAS）提供了关于控制重要经济性状的等位基因的频率和分布的有价值的信息。当登录号可以从接近1，000增加到接近10，000或更多时，这些分析的价值会大大增强。本研究首次对14，000份大豆材料[Glycine max（L.）Merr.和G. [Soja Siebold & Zucc.]使用50 K-SNP芯片。来自日本的加入相对同质，与韩国的加入不同。总体而言，日本和韩国的加入量与中国的加入量存在差异。美国种质资源创建者的祖先主要来自两个中国亚群，这反映了美国种质资源的整体组成。对种子蛋白质和油进行的12，000次GWAS是迄今为止在植物中报道的最大的，并在20号和15号染色体上鉴定出具有强信号的单核苷酸多态性（SNP）。先前报道的对蛋白质和油含量重要的20号染色体区域进一步缩小，现在只包含三个可能的候选基因。单倍型效应显示该位点的油分与蛋白质含量呈强负相关，表明该位点存在负多效性效应或多个紧密连锁的位点处于排斥相连锁。绝大多数的加入携带单倍型等位基因赋予低蛋白质和高油。我们的研究结果提供了一个更全面的了解美国农业部大豆收集的遗传变异的分布，以及它如何与经济上重要的性状的表型变异。
Population structure analyses and genome-wide association studies (GWAS) conducted on crop germplasm collections provide valuable information on the frequency and distribution of alleles governing economically important traits. The value of these analyses is substantially enhanced when the accession numbers can be increased from similar to 1,000 to similar to 10,000 or more. In this research, we conducted the first comprehensive analysis of population structure on the collection of 14,000 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold & Zucc.] using a 50K-SNP chip. Accessions originating from Japan were relatively homogenous and distinct from the Korean accessions. As a whole, both Japanese and Korean accessions diverged from the Chinese accessions. The ancestry of founders of the American accessions derived mostly from two Chinese subpopulations, which reflects the composition of the American accessions as a whole. A 12,000 accession GWAS conducted on seed protein and oil is the largest reported to date in plants and identified single nucleotide polymorphisms (SNPs) with strong signals on chromosomes 20 and 15. A chromosome 20 region previously reported to be important for protein and oil content was further narrowed and now contains only three plausible candidate genes. The haplotype effects show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects or multiple closely linked loci in repulsion phase linkage. The vast majority of accessions carry the haplotype allele conferring lower protein and higher oil. Our results provide a fuller understanding of the distribution of genetic variation contained within the USDA soybean collection and how it relates to phenotypic variation for economically important traits.