Genetic diversity and marker-trait association analysis for grain quality, yield and yield attributes in hill rice (Oryza sativa L.)

The studies on genetic diversity and marker-trait association analysis of north-eastern hill rice for grain quality and yield attributes are of enormous importance for the identification of promising rice genotypes with better grain and cooking quality. Genetic diversity among 130 rice genotypes of North East India and marker-trait association was assessed using genotypic data of 90 SSR markers and phenotypic data. The phenotypic diversity analysis showed considerable variation across genotypes for grain quality and yield-attributing traits. Population structure analysis, distance-based neighbor joining cluster and principal coordinate analysis using genotypic data grouped the genotypes into two sub-populations. Analysis of molecular variance and pairwise FST values showed significant differentiation among all the pairs of sub-populations. Marker trait association analysis revealed a total of six associations at p < 0.0001 for grain quality and yield attributing traits with R2 ranging from 3.55 to 11.91% under the upland ecosystem. The present study validated the association of the RM240 marker with Gel consistency and plant height gene on chromosome 3. The study indicated the presence of novel QTLs for days to maturity with RM210 and RM105 and days to flowering with RM101.