Genetic diversity and marker trait association analysis for grain quality, yield and yield attributes in hilly rice of North-Eastern Himalayan region

Abstract

Abstract Background: The demand for quality rice is increasing due to the influence of population growth and rising living standards. North eastern region of India is considered as centre of origin of rice and has diversified rice landraces with unique cooking quality and yield attributing traits. The studies on genetic diversity and marker-trait association analysis of north-eastern hilly rice for grain quality and yield attributes are of enormous importance for the identification of promising rice genotypes with better grain and cooking quality vis a vis markers associated with grain quality and yield attributes. This will assist in development of high-yielding cultivars. Results: 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, yield and yield-attributing traits. The principal component analysis revealed that plant height, panicle length, spikelet fertility, decorticated grain length and width, days to maturity, days to 50% flowering, and grain yield govern the diversity. Population structure analysis, distance-based neighbour 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-population. Marker trait association analysis using the mixed linear model 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 RM240 marker with Gel consistency for use in MAS and existence of 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 under consideration. Conclusions: The present study suggests that the diverse germplasm of NE India and identified markers could be used in rice breeding programs for the improvement of grain quality and yield attributes.