Genome-wide association study identifies QTLs conferring salt tolerance in rice

Rice is the most important cereal crop but is sensitive to salinity stress. Increased salinization is progressively reducing rice productivity, escalating calls for research to ensure sustainable food production. The genetic diversity available in cultivars provides a rich resource for discovering genes associated with salt tolerance which has not yet been sufficiently utilized. In this study, 54 QTLs associated with salt tolerance were detected through genome-wide association study (GWAS) using a core population consisting of 181 cultivars. We detected 17 loci significantly associated with dry weight ratio (DWR) for salt tolerance. In the region of a novel QTL qST-7.19 on chromosome 7, we identified a candidate gene encoding a multidrug and toxic compound extrusion (MATE) protein and further validated the effect by using near-isogenic line of the candidate gene. These QTLs and the candidate gene pave the ways for salinity tolerance improvement through molecular breeding.