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

Qureshi S.A. Sarıkaya M.F. Nadeem M.A. Ali A. Mortazavi P. Bedir M. Tatar M. Madenova A. Kabylbekova B. Ali F. Altaf M.T. Soltanbekov S. Tokibayev S. Ilyas M.K. Kökten K. Baloch F.S.
December 2025 BioMed Central Ltd

BMC Plant Biology
2025 #25 Issue 1

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.

Genetic diversity assessment , Germplasm characterization , IPBS-retrotransposon markers , Lentil , Molecular breeding resources , Population structure analysis

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Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, 58140, Turkey
Department of Biotechnology, Faculty of Science, Mersin University, Mersin, 33343, Turkey
Kazakh Fruit and Vegetable Research Institute, Almaty, 050060, Kazakhstan
Kazakh National Agrarian Research University, Almaty, Kazakhstan
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Hainan, Sanya, 572025, China
Department of Field Crops, Faculty of Agriculture, Recep Tayyip Erdoğan University, Rize/Pazar, Turkey
LLP Research Center for Bio and IT Technologies, Almaty, Kazakhstan
National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, South Korea

Faculty of Agricultural Sciences and Technologies
Department of Biotechnology
Kazakh Fruit and Vegetable Research Institute
Kazakh National Agrarian Research University
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication)
Department of Field Crops
LLP Research Center for Bio and IT Technologies
National Agricultural Research Centre
Department of Plant Resources and Environment

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