Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA.
Sci Data. 2021 Feb 8;8(1):50. doi: 10.1038/s41597-021-00834-w.
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
我们报告了 481 个不同大豆品种（包括 52 个野生大豆[Glycine soja]和 429 个栽培大豆[Glycine max]品种（地方品种和精英品种））的重测序结果，揭示了大豆的遗传多样性和结构特征。利用这些数据，我们鉴定了 780 万个 SNP，预测了 SNP 相对于基因区域的效应，并鉴定了遗传结构、亲缘关系和连锁不平衡。我们发现了不同地理区域选择不同谱系的明显的、大多独立的证据。在栽培品种中，我们鉴定了许多高度保守的区域，这表明在驯化过程中发生了选择。与用 SoySNP50K iSelect BeadChip 全基因组分型的美国种质资源相比，这些品种中有超过 95%与 SoySNP50K 对应的品种具有高度相似性。大约 5%的品种可能存在种子来源或基因型跟踪的错误。
