Genome-wide SNP discovery using ddRADseq reveals candidate loci associated with salinity tolerance in rice

Salt stress is a major constraint to rice production in saline environments, necessitating the development of salt-tolerant varieties through molecular breeding approaches. This study aimed to identify functional genetic variations associated with salinity tolerance in contrasting rice genotypes using double-digest RAD sequencing (ddRADseq). Seven rice lines with contrasting responses to salinity stress were analyzed, including FL478, a tolerant variety, and IR64, a sensitive check. Salinity stress was applied at the seedling stage with 0, 50, 100, and 150 mM NaCl, and genotypes were classified based on their performance under 150 mM NaCl. A total of 7,980,092 high-quality reads were generated, of which approximately 83% aligned to the rice reference genome. Genome-wide analysis identified 80,159 SNPs and 6,403 InDels among the seven rice genotypes, with 42% of SNPs located in genic regions. Comparative analysis between tolerant and sensitive genotypes revealed 138 non-synonymous SNPs (nsSNPs) (between FL478 and IR64) within 116 abiotic stress-related genes in coding regions, potentially affecting protein function. These candidate genes and functional variants are likely associated with salinity tolerance mechanisms in rice. The identified nsSNP markers effectively distinguished tolerant and sensitive genotypes and provided valuable resources for marker-assisted selection and the development of salt-tolerant rice varieties.