Association Mapping of Drought Avoidance and Agronomic Traits in Rice (Oryza Sativa L.) Landraces with SSR Markers and Genotyping-By-Sequencing Approach
Abstract Development of rice varieties suited to varying drought stress level, and crop stages, relies mainly on identifying new genetic resources and genomic targets to improve whole plant physiological processes and productivity. This study with 99 rice germplasm adapted to Southwestern Indian peninsular region genotyped with 100 SSR markers evaluated over five different seasons/field trials to characterize plant physiological, root traits and yield related traits under different intensity and crop stage experienced water limitation. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Genome-Wide Association Study revealed genetic variation and genomic targets underlying major QTLs for different physiological, root and plant production traits. Combined analysis with trials 1-4 revealed 14 genomic regions governing multiple traits that contribute to plant performance and productivity under water stress. Genetic characterization of nine selected landraces and two elite cultivars using genotyping-by-sequencing (GBS) revealed haplotype variation within genomic targets on chromosome 1, 4, 6 and 11 for potential use as molecular markers. The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars.