Unveiling genetic diversity and population structure in lentil (Lens culinaris) germplasm through scot markers

Background: Lentil (Lens culinaris) is extensively cultivated for its edible seeds and plays an important role in food security and sustainable agriculture. Understanding the genetic diversity and population structure of lentil germplasm is crucial for breeding programs and for effective conservation of genetic resources. Methods and results: In this study, the genetic variation and population structure of 96 lentil accessions were assessed using Start Codon Targeted (SCoT) markers. Fifteen polymorphic primers generated a total of 440 bands, with an average of 29.33 bands per primer. The overall polymorphism percentage was 93.38%. Genetic diversity parameters including, including polymorphism information content (ranging from 0.25 to 0.86), effective number of alleles (1.28–1.61), gene diversity (0.18–0.36), and Shannon’s information index (0.29–0.54), revealed substantial genetic variability among the accessions. Molecular variance analysis showed that 87% of the genetic variation occurred within populations. STRUCTURE analysis grouped accessions into four populations (A, B, C, and D). This clustering was further supported by principal coordinate analysis (PCoA) and neighbor-joining, which differentiated genotypes based on their geographic origins. Conclusion: SCoT marker analysis revealed considerable genetic diversity among the lentil germplasm evaluated. Notably, the accessions Pakistan2 and Iran3 exhibited the greatest genetic distance from others, indicating their potential value as parental lines for future lentil breeding and improvement programs.