Genome-wide association study (GWAS) to identify novel SNPs associated with salinity tolerance in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is widely considered a salt-sensitive crop, although considerable genetic diversity for salinity tolerance has been documented. Salinity is a serious constraint in arid and semi-arid regions, severely limiting agricultural productivity. This stress inhibits seed germination, hinders nodule formation, slows vegetative growth, and ultimately reduces yield. Salinity-induced damage is primarily caused by osmotic stress, which reduces water uptake, and ion toxicity, which impairs embryo viability and plant physiology. Three hundred chickpea genotypes were tested in two different trials for germination performance under controlled greenhouse conditions at the Agricultural Research Centre (ARC) in Giza. Salinity stress was induced in a hydroponic system with 80 mM NaCl, while hydroponic water was used as the control treatment. Population structure analysis divided the chickpea germplasm into four distinct sub-populations. A genome-wide association study (GWAS) for trial one identified four single nucleotide polymorphisms (SNPs) on chromosome 4 that are strongly associated with salinity tolerance: SNP 4:45,418,897, SNP 4:45,419,000, SNP 4:45,422,161, and SNP 4:45,439,709. For trial two, three SNPs on chromosome 4 were also strongly associated with salinity tolerance: SNP 4:45,417,959, SNP 4:45,419,000, and SNP 4:45,422,025. In the combined analysis, three significant SNPs were identified on chromosome 4: SNP 4:45,418,986, SNP 4:45,419,000, and SNP 4:45,421,876.