Genotyping by Sequencing of the Pea PSP Collection

Over the past decade, the ability to generate large sets of single nucleotide polymorphisms (SNPs) at low cost using next-generation sequencing (NGS) technologies has greatly expanded the capacity for trait mapping, germplasm characterization, and marker-assisted and genomic selection in many crop species. For pea (Pisum sativum), we report the use of genotyping-by-sequencing (GBS) to generate tens of thousands of SNP markers in 380 individuals comprising a subset of the USDA Pea PSP collection, a population that includes single plant derived accessions from the refined core collection, along with breeding lines, USDA RIL parents, and Pisum sativum subspecies. Raw sequences from individuals were filtered by read depth and quality, and SNPs were filtered by minor allele frequency, sample call rate, and Hardy-Weinberg equilibrium for a population of inbreds. GBS-derived SNPs are enriched in genic regions, and may be able to efficiently tag QTL identified through linkage or association mapping studies. These SNPs represent a valuable resource for the genetic characterization of the highly phenotyped PeaPSP collection, and the methods used to generate SNP markers in this population are easily transferrable to other populations.