Field performance and genetic diversity analysis of biparental pea lines (Pisum sativum L.) using SSR and InDel markers

Enhancing pea (Pisum sativum L.) productivity under rainfed conditions requires the identification of high-performing and genetically diverse genotypes to support sustainable breeding programs. The agronomic performance and genetic diversity of fifteen pea genotypes, including eleven biparental lines advanced to the F₇ generation and their four parental genotypes, were evaluated over two consecutive growing seasons under natural rainfed conditions. Seed yield and yield-related traits were analyzed using two-way analysis of variance, while genetic diversity was assessed using sixty-six simple sequence repeat (SSR) and insertion-deletion (InDel) markers and analysis of molecular variance (AMOVA). Nine of the eleven biparental lines produced significantly higher seed yield than at least one parental genotype (P ≤ 0.05). OR-M04 (G4) recorded the highest mean seed yield (22.7 g plant-¹), exceeding the best parent (10.2 g plant-¹) by 122.6%, followed by OR-M06 (G6) and OR-M07 (G7). Molecular analysis revealed moderate genetic variation, with polymorphic information content values ranging from 0.117 to 0.710 and 2–6 alleles detected per locus. Clustering analysis grouped the genotypes into five distinct clades. AMOVA attributed 24% of total molecular variation among inferred clusters (FST = 0.242, P = 0.001), indicating moderate genetic differentiation. The eleven F₇ biparental lines were genetically and phenotypically distinct from their parents, highlighting several lines with strong potential for future variety development and pea breeding under rainfed environments.