Revealing the genetic diversity and population structure in lentil (Lens culinaris) germplasm using inter-primer binding site (iPBS)-retrotransposon markers.

BACKGROUND: Lentil (L. culinaris ssp. culinaris) is a climate-resilient legume crop that plays a key role in global food security and sustainable agriculture. Understanding genetic diversity and population structure is essential for conserving genetic resources, enhancing breeding strategies, and developing improved, high-performing cultivars. RESULTS: The genetic diversity and population structure of 96 lentil genotypes were evaluated using 15 iPBS-retrotransposon markers, which produce a total of 346 scorable bands. Among these primers, iPBS-2376 yielded the highest number of bands (33). The polymorphism information content (PIC) values ranged from 0.17 to 0.38, indicating a broad range of marker informativeness. Genetic diversity analysis revealed a mean gene diversity (h) of 0.29, a Shannon information index (I) of 0.44, and an effective number of alleles (Ne) of 1.48. The maximum genetic distance (0.88) was observed between genotypes G25 (Pakistan25) and G94 (Cagil), reflecting this genetic divergence. Analysis of molecular variance (AMOVA) revealed that 82% of the total variation occurred within populations. The STRUCTURE analysis and neighbor-joining (NJ) clustering consistently grouped the genotypes into two distinct clusters, largely corresponding to their geographic origins. Similarly, Principal Coordinate Analysis (PCoA) further confirmed this separation based on geographic distribution. CONCLUSIONS: These results demonstrate considerable genetic diversity within the lentil germplasm. This suggests that these accessions can be employed in breeding programs to design improved lentil cultivars with enhanced resilience, higher crop output, and broader adaptability.