Candidate gene based association analysis of salt tolerance in traditional and improved varieties of rice (Oryza sativa L.)

Rice is a staple food for more than half of the world population but the productivity of rice plant is attenuated in salt-stressed environment. Here 69 diverse rice varieties were evaluated for their salt tolerance capacity. Tolerant and susceptible genotypes were differentiated based on their standard evaluation score and thirteen other physiological parameters. A genome wide 48-SNP markers chip was used to analyze genetic diversity and population structure of the genotypes. Thirteen different salt-responsive candidate genes belonging to different functional categories including transporters, metabolic pathways, intermediate genes and transcription factors were amplified and re-sequenced using Ion Torrent PGM platform. Total 155 SNPs were identified in the selected 13 genes. A candidate gene based association analysis found seven-marker trait associations with five salt tolerance traits. From the 13 genes analyzed, DUF 6 was associated with Na+/K+ ratio, root biomass and root dry weight; SOS 1 with Na+ concentration in leaves and HKT 2;4 with shoot dry weight. This study will be helpful in the development of functional markers associated with salt stress tolerance in rice.