Bandillo Nonoy, Jarquin Diego, Song Qijian, Nelson Randall, Cregan Perry, Specht Jim, Lorenz Aaron
Dep. of Agronomy & Horticulture, Keim Hall, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583-0915.
Soybean Genomics and Improvement Lab., Beltsville Agricultural Research Center, Beltsville, MD, 20705.
Plant Genome. 2015 Nov;8(3):eplantgenome2015.04.0024. doi: 10.3835/plantgenome2015.04.0024.
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 ∼1,000 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.
对作物种质资源库进行的群体结构分析和全基因组关联研究（GWAS），可为控制经济重要性状的等位基因的频率和分布提供有价值的信息。当种质资源数量从约1000份增加到约10000份或更多时，这些分析的价值将得到显著提升。在本研究中，我们使用50K-SNP芯片，对14000份大豆种质资源[大豆（Glycine max (L.) Merr.）和野生大豆（G. soja Siebold & Zucc.）]进行了首次全面的群体结构分析。源自日本的种质资源相对同质，且与韩国的种质资源不同。总体而言，日本和韩国的种质资源均与中国的种质资源有所分化。美国种质资源的奠基者祖先大多来自两个中国亚群，这反映了美国种质资源的整体构成。对12000份种质资源进行的种子蛋白和油含量的GWAS是迄今为止在植物中报道的规模最大的研究，该研究在20号和15号染色体上鉴定出了具有强信号的单核苷酸多态性（SNP）。先前报道的对蛋白和油含量重要的20号染色体区域进一步缩小，现在仅包含三个可能的候选基因。单倍型效应表明，在该位点油和蛋白之间存在强烈的负相关关系，这表明存在负向多效性效应或处于相斥相连锁的多个紧密连锁位点。绝大多数种质资源携带赋予较低蛋白和较高油含量的单倍型等位基因。我们的研究结果更全面地了解了美国农业部大豆种质库中所含遗传变异的分布情况，以及它与经济重要性状表型变异之间的关系。
