Genotyping by Sequencing Reveals the Genetic Diversity of the USDA Pisum Diversity Collection

The USDA Pisum Diversity Collection, UPDC, is a unique resource that represents the breadth of the genetic diversity of the genus in an inbred format that facilitates genetic study. The UPDC includes inbred accessions from the refined pea core collection, parent lines of USDA recombinant inbred (RIL) populations, accessions from U.S. pea breeding programs, Pisum sativum subspecies, and the wild species, Pisum fulvum, from diverse geographies worldwide. Genetic characterization of the UDPC is useful in order to evaluate its potential as a community resource for trait mapping and breeding. In this study, genotyping-by-sequencing was used to sequence 477 Pisum spp. accessions belonging to the UPDC. Over 10,000 SNPs were called, and a linkage map derived from a biparental RIL population of ‘Aragorn’ x ‘Kiflica’ was used to anchor a subset of these SNPs for downstream applications such as genome-wide association mapping and the elucidation of alleles contributing to structural variation within the collection. The largest amount of genetic variation was contained in accessions belonging to subgroups that consisted of wild species and subspecies, highlighting the value of these accessions as a source of diversity to enrich the otherwise narrow genetic base of cultivated pea.