Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection

Abstract

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.