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

Background Lentil ( Lens culinaris ) is widely cultivated for its edible seeds and plays an important role in food security and sustainable agriculture. Understanding genetic diversity and population structure of plant material is essential for their genetic resources in breeding programs and for guiding germplasm conservation efforts. Methods and results This study evaluated the genetic variation and population structure of 96 lentil accessions using SCoT markers. A total of 440 bands were generated by 15 polymorphic primers, averaging 29.33 bands per primer. The overall polymorphism percentage was 93.38%. The diversity parameters including polymorphism information content (0.25–0.86), effective number of alleles (1.28–1.61), gene diversity (0.18–0.36), and Shannon’s information index (0.29–0.54) confirmed significant genetic variability in germplasm. The results from molecular variance analysis showed that 87% of the genetic variation occurs within populations. The STRUCTURE analysis partitioned the lentil accessions into 4 populations (A, B, C, and D). Principal coordinate analysis and neighbor-joining also distinguished the genotypes based on their collection sites. Conclusion SCoT marker analysis showed significant genetic diversity among the lentil germplasm studied. The accessions Pakistan2 and Iran3 exhibited greater genetic distance which suggests their suitability as parent lines for use in future lentil improvement programs.