Diversity Analysis, Population Structure and Association Mapping for Grain Quality and Yield traits in Lowland rice of Nagaland, India using SSR markers

North-east India is known for the hot spot of rice species in the world. Nagaland alone harbor great diversity of rice and possessed immense potential of rice production. In this study, 81 genotypes across the state including 2 commercial varieties were evaluated for diversity studies, a total of 102 alleles, 13% variation among the population, 87% variation among the individuals, 0% variation within the individual, PIC value of 40 SSR markers from 0.23 to 0.99 were observed. The whole accessions were divided into two main group through STRUCTURE and an unweighted neighbour-joining cluster analysis. In PCoA, the total variation of the first three axes of differentiation was 17.37%. A total of 59 association between traits and markers was observed, among these, association between RM209, RM6836, RM247, RM440, RM3575 and grain dimension; RM5709 and RM3331 with flowering and grain yield have been reported. The observed genetic diversity, population structure and association between traits and markers can be useful in further improvement of rice grain quality and yield using the collected germplasm. This will aid in breeding superior variety that can benefit the state as well as the region in increase production of quality rice.