Structure in the USDA Soybean Germplasm Collection

The 50k SNP genotypes for the USDA soybean germplasm collection is a public data resource that was recently made available for about 20,000 accessions. We combined the genotypes with phenotypic and passport data to elucidate structure in the collection and develop genome-wide predictions for selection. A phylogenetic analyses confirms the known lack of diversity in soybean germplasm. Genotypic clustering through principle component analyses reflects known variation. In particular, maturity is the gateway to all other traits in soybean.