Molecular characterization of lentil (lens culinaris) germplasm

Lentil is a vital legume crop with nutritional, agricultural, and economic importance, especially in arid and semi-arid regions. However, the narrowing genetic base due to domestication bottlenecks necessitates comprehensive molecular characterization. This study aimed to assess the genetic diversity and population structure of 96 lentil (Lens culinaris) genotypes using two molecular marker systems: Inter-Primer Binding Site (iPBS) and Start Codon Targeted (SCoT) markers A total of 15 polymorphic primers from each marker system were selected based on their high amplification clarity and polymorphism. The iPBS markers produced 346 bands with 95.25% polymorphism, while SCoT markers yielded 440 bands with 93.38% polymorphism, indicating a high level of genetic variation among the genotypes. Population structure analyses using STRUCTURE, Neighbor-Joining clustering, and Principal Coordinate Analysis (PCoA) revealed well-defined genetic groupings, partially corresponding to geographic origins. Analysis of Molecular Variance (AMOVA) showed that the majority of the genetic variation resided within populations rather than between them. Genotypes from Pakistan exhibited the highest genetic diversity in both marker systems. These findings confirm the effectiveness of iPBS and SCoT markers in dissecting lentil genetic diversity and offer valuable insights for breeding programs, germplasm conservation, and future genomic studies targeting stress tolerance and yield improvement.