Genetic diversity assessment of edible-podded peas (Pisum sativum var. saccharatum and Pisum sativum var. macrocarpon) using morphological traits and SSR markers

Edible-podded peas viz., snow peas and sugar snap peas are valued for their tender edible pods, nutritional quality, export potential and increasing market demand. However, limited information is available regarding their genetic diversity and population structure. Therefore, the present study was undertaken to assess agro-morphological and molecular diversity among 25 edible-podded and two garden pea genotypes under field conditions during 2022–2024. Genetic diversity was evaluated using 27 phenotypic traits comprising 14 qualitative and 13 quantitative descriptors based on DUS guidelines, along with 40 SSR markers through Shannon Diversity Index, Mahalanobis D² statistics, principal component analysis, cluster analysis, AMOVA and STRUCTURE analysis. Among qualitative traits, pod curvature showed highest variability (Shannon Diversity Index, H = 1.25) followed by seed colour (H = 1.21). Mahalanobis D² analysis grouped genotypes into 5 clusters, with highest inter-cluster distance (2061.31) among Cluster III (PED-18-1, PED-18-7, PED-21-6, Arka Sampoorna) and Cluster V (Him Palam Mithi Phali-2, Honey Snap, PED-21-2, Oregon Sugar Pod, PED-21-3, Royal Snow, Tarvedo Sugar), indicating considerable genetic divergence. Out of 40 SSR markers screened, 16 were polymorphic and generated 2–6 alleles per locus with moderate to high polymorphic information content of 0.50, while primer AA332 exhibited the highest PIC value (0.77). SSR-based clustering grouped the genotypes into two major clusters with distinct sub-clustering patterns. AMOVA revealed 91% of the genetic variation existed within populations and STRUCTURE analysis identified four subpopulations (K = 4), indicating moderate genetic heterogeneity among the genotypes. Based on the combined agro-morphological and SSR marker analyses, PED-18-1, PED-18-7, PED-21-6, Arka Sampoorna, and PED-21-2 emerged as the most distinct genotypes and represent valuable parental resources for edible-podded pea improvement. These genotypes can be utilized to enhance productivity, strengthen food and nutritional security and promote sustainabe breeding in pea growing regions.