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.

Genome-Wide association study uncovers pea candidate genes and pathways involved in rust resistance

“…Plant material consisted in a diverse core collection of 320 Pisum accessions of worldwide origin gathered previously at Institute for Sustainable Agriculture – CSIC to ensure an extensive range of characteristics in terms of phenotype and their genetic makeup (Rispail et al 2023). The collection includes accessions that have already demonstrated their potential for resistance to several pea diseases including rust (accessions IFPI3260, PI347352, PI347343, PI347353 and PI347389) (Barilli et al 2009a).…”

“…The process of DNA extraction, DArTseq protocol, and data analysis were previously detailed in Rispail et al (2023). In summary, the genotyping of the pea core collection was carried out using the DArTSeq approach, as described by Barilli et al (2018).…”

“…Based on the linkage disequilibrium resulted in this pea core collection described by Rispail et al (2023), we considered genes either containing a DArTseq marker or residing within a 30 kb window from the marker as putative candidate genes.…”

Challenges in pea breeding for tolerance to drought: Status and prospects

“…Several studies have shown genetic diversity in Pisum germplasm (Annicchiarico, Romani, et al, 2017; Rispail et al, 2023; Smýkal et al, 2011; Yang et al, 2022). The primary gene pool for domesticated peas consists of P. sativum , its subsp.…”

“…The high diversity of key traits in wild and domesticated peas is promising for the strategic crossing of complementary genotypes. This variation is an essential source of desired alleles in the agronomic, physiological and biochemical traits to improve drought adaptation and yield gains in other pea crops (Rispail et al, 2023; Smýkal et al, 2018; Yang et al, 2022).…”