Multi-season hydroponic phenotyping and multi-model genome wide association mapping identifies genomic regions and putative candidate genes associated with seedling-stage salinity response in chickpea

Chickpea ( Cicer arietinum L.) is sensitive to salinity stress, particularly at the seedling stage. To dissect the genetic basis of seedling-stage salinity response, a globally representative chickpea reference set was evaluated under hydroponic conditions across two growing seasons alongside a tolerant check (CSG 8962). Eighteen morpho-physiological and ionic traits were quantified, and data from both seasons were analysed through genome-wide association studies (GWAS) using five statistical models implemented in GAPIT 5.0. Seven single-nucleotide polymorphisms (SNPs) consistently associated with five salinity-response traits were identified, with several residing within genomic regions linked to growth regulation, ion transport, and reactive oxygen species (ROS) homeostasis. The expression of selected genes proximal to significant loci— CaROS1L , CaCYP450 , CaOPR11 , CaCCX4 , CaAKT2/3 , CaCML11 , CaGRF5L , and CaMOBKL1A —was further assessed in contrasting genotypes under control and salt stress, revealing distinct transcriptional responses between tolerant and least tolerant lines. Genes such as CaCML11 (associated with calcium signalling) and CaOPR11 (associated with hormone signalling) exhibited higher expression in tolerant lines, suggesting their potential involvement in salinity response mechanisms. These findings highlight genomic regions and candidate genes that may contribute to early-stage salinity response and offer valuable molecular resources for chickpea improvement.