Abstract
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.
Highlights
Background & SummarySoybean [Glycine max (L.) Merr.] is one of the major grain legumes and oil seeds cultivated worldwide, in Asia and the Americas
The first reference genome for cultivated soybean was released in 20104, followed by high-quality assemblies of several other soybean accessions, including elite lines and wild soybean accessions[5,6,7,8,9,10]. This genomic sequencing has been complemented by resequencing projects, designed to assess genetic variation across broader samplings of soybean germplasm[3,5,12,13]
The germplasm of the 481 accessions comes from 37 countries, with the largest numbers coming from China (223), Japan (56), the U.S (54), South Korea (44), the Russian Federation (26), and North Korea (14)
Summary
Background & SummarySoybean [Glycine max (L.) Merr.] is one of the major grain legumes and oil seeds cultivated worldwide, in Asia and the Americas. The USDA Soybean Germplasm Collection contains 20,035 accessions, including 1,168 G. soja and 18,867 G. max lines. The SoySNP50K BeadChip[14] was utilized for genotyping these accessions and for selecting a core set of diverse G. max (1,148) and G. soja (81) lines for further studies.
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