Genome wide association mapping reveals genetic loci and candidate genes for seedling stage drought tolerance in lentil (Lens culinaris)

Abstract

Lentil (Lens culinaris) is a very important cold-season nutritious legume crop. The crop faces intermittent drought in South Asian countries and terminal drought in West Asian and North African Mediterranean regions causing adverse impact on lentil productivity. The present study aimed to evaluate a diverse lentil panel (243 genotypes) under irrigated and drought conditions at seedling stage and to identify significant marker trait associations for drought tolerance traits. Drought stress was imposed by restricting the pre-sowing irrigation. A total of 18 different morpho-physiological traits including root (length, surface area, volume, tips and forks), physiological (germination percentage, NDVI, canopy temperature) and growth (seedling vigor, plant biomass) traits were recorded among the lentil genotypes in both control and stress conditions. All the traits except canopy temperature were found to be significantly reduced under stress. Principal component analysis explained 56.3 % variation in control and 60.7 % variation in drought condition. Shoot dry weight had significant correlation to NDVI, shoot branching, primary and total root length, and root length density. Genotypes IC560032, IC560246, P3227, IC560051, and IG134349 were identified as drought-tolerant using SSI (<0.5). Association mapping analysis identified 65 and 71 non-overlapping distinct SNPs significantly associated with all traits under control and drought conditions, respectively. Putative candidate genes encoding legumain-like cysteine endopeptidase, L-ascorbate oxidase, and auxin-responsive proteins were involved in the regulation of key drought tolerance associated traits like germination percentage, root length, seedling vigor respectively. These findings highlight the potential of lentil germplasm for drought resilience and provide a valuable genetic resource for breeding high-yielding, stress-tolerant varieties.