SSR-based genetic diversity and population structure analysis of 144 core pea (Pisum sativum L.) accessions

Pea (Pisum sativum L.), a widely cultivated cool-season legume crop globally, serves as a high-quality source of plant protein for humans. Despite its critical importance, systematic evaluations of the genetic diversity and population structure of a phenotype-guided core collection integrating germplasm from multiple regions remain limited. In this study, a core collection of 144 pea accessions with important breeding value was evaluated for genetic diversity using Simple Sequence Repeat (SSR) molecular markers to elucidate their population genetic structure. The genetic diversity results revealed an average number of alleles (Na) of 4.923, an average number of effective alleles (Ne) of 2.130, an average expected heterozygosity (He) of 0.468, and an average observed heterozygosity (Ho) of 0.207. The average Shannon's information index (I) and average polymorphism information content (PIC) were 0.895 and 0.4219, respectively, indicating relatively rich genetic diversity within the pea population. Population structure analysis (K = 2) divided the accessions into two major genetic groups, with 32 accessions assigned to Group I, 61 to Group II, and 51 accessions (35.4%) showing admixed ancestry. The UPGMA dendrogram and principal component analysis were broadly consistent with this grouping. Analysis of molecular variance (AMOVA) revealed that most genetic variation was distributed within populations (87%), whereas variation among populations accounted for 13% (Fst = 0.129, P < 0.001). These findings provide a genetic stratification framework that can guide germplasm conservation, parental selection, and future marker-assisted breeding efforts in pea.