Insights into the genetic diversity of chilli pepper (Capsicum annuum L.) using morphological traits and microsatellite markers

Gene pool diversity is being reshaped due to preference of stakeholders for varieties with specific traits, along with government policies that place greater responsibility on breeders to preserve and enhance genetic diversity which is an essential component of crop improvement programs. Keeping this in view, the present investigation was undertaken to assess morphological and molecular diversity using nine morphological descriptors, 35 quantitative traits, and 60 simple sequence repeat (SSR) markers across a collection of 32 chilli pepper genotypes. Seven morphological descriptors were discovered to be polymorphic, with the intensity of anthocyanin color of nodes having the greatest Shannon diversity index (0.95). The studied genotypes were divided into seven groups by Mahalanobis D ² with the maximum inter-cluster distance (48.98) between clusters V and VI and the highest intra-cluster distance by cluster V (30.33). The marketable red ripe fruits per plant made the greatest contribution to genetic divergence (23.99%). Molecular markers revealed wide diversity among genotypes with average polymorphism of 0.426 and the polymorphic information content (PIC) varied from 0.154 to 0.847 with primer BM 61910 having maximum PIC representing their efficacy in detecting genetic diversity. Based on SSR data using the UPGMA approach and structural analysis, 32 genotypes were categorized into two major clusters, resulting in three distinct population groupings. In addition, based on their genetic similarities and geographic origin the neighbor-joining tree inferred three groupings. This study provides essential insights into morphological and molecular markers, highlighting their significance in assessing genetic diversity and their potential application in chilli breeding and genetic improvement.