Comparative Genome-Wide Association Studies for Plant Production Traits under Drought in Diverse Rice (Oryza sativa L.) Lines Using SNP and SSR Markers

Rice is the major staple food crop for more than half of the world's population, but its productivity is often reduced by drought, especially when grown under rainfed conditions. Identification of molecular markers associated with plant production traits under drought, especially in the target populations of the environment (TPE) presents an opportunity to improve rainfed rice production using genomics tools. Marker-trait associations were studied using 1168 simple sequence repeat (SSR) markers and 911,153 single nucleotide polymorphisms (SNPs) with 17 diverse rice lines from different geographical regions and hydrological habitats. STRUCTURE analysis discriminated the rice accessions into three subpopulations. Significant genotypic linkage disequilibrium (LD) was found in the rice accessions using SSR markers. A total of 130 and 118 water-trait associations were obtained with SSR and SNP markers respectively, under stress. Comparison of SSR and SNP marker-trait associations revealed 23 consistent associations. Five marker-trait associations with genic SNPs were observed out of 23 associations. These genomic regions may be potential candidates for application in marker-assisted breeding of rice cultivars suitable for water-limited environments.