Genetic analysis for detection of genes associated to drought tolerance in rice accessions belonging to north east India

Introduction The North East (NE) India is rich in biodiversity and also considered as the secondary centre for origin of rice. The NE rice accessions was characterized previously using genetic markers and morphological traits. Simultaneously, genome-wide association studies (GWAS) reveal significant marker-trait associations for the drought tolerance traits. Methods and results The genetic diversity and population structure of 296 NE rice accessions were studied using 96,712 single nucleotide polymorphism (SNP) markers distributed across 12 chromosomes. The accessions were clustered into two major sub-groups (SG). A total of 91 accessions were assembled as SG1 and 114 accessions as SG2, while the remaining 91 were admixture genotypes. A total of 200 genotypes belonging to different groups were phenotyped for yield component traits under drought and control conditions. The GWAS was performed to identify significant marker-trait associations (MTAs). Consequently, 47 MTAs were detected under drought, exhibiting 0.02–9.95% of phenotypic variance (P.V.). Whereas 58 MTAs were discovered under control conditions, showing a 0.01–9.74% contribution to the phenotype. Through in-silico mining of QTLs, 2999 genes were identified. Among these; only 22 genes were directly associated with stress response. Conclusion These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in popular drought susceptible rice varieties.