Rice GWAS reveals key genomic regions essential for salinity tolerance at reproductive stage

Salt tolerance is an important complex trait in rice which helps the plant to survive under salt stress condition. The complexity of salt tolerance is governed by many genes which could be identified efficiently by genome wide association study (GWAS). In the present study, we evaluated 180 diverse rice accessions for salinity tolerance at reproductive stage and successfully genotyped them using simple sequence repeats markers covering all 12 chromosomes. Eleven physiological parameters which include Na+, K+, Ca2+, Mg2+ content in stem and leaves and two important morphological traits grain yield and salt injury score were measured under control and saline conditions at reproductive stage. Population structure analysis revealed four subgroups and admixture level ranged from 0.70 to 57.2%. Association study using mixed linear model controlling both structure and kinship, identified 28 significant marker-trait associations and out of which 19 associations were identified for Na+, K+, Na+/K+ uptake in stem and leaves. The phenotypic variance for these associations ranged from 5.12 to 13.37%. The position of several associated markers was found close to candidate genes like transcription factors, membrane transporters, signal transducers which have previously shown to play active roles of salinity tolerance in rice. The present GWAS was successful in unravelling genomic regions that regulate ionic homoeostasis in rice. Furthermore, the salinity tolerant accessions identified during the screening could become important resource for breeding programs.