Genetic diversity and marker-trait association analysis in Manipur rice germplasm using microsatellite markers

The loss of rice's genetic diversity caused by the replacement of landraces with superior cultivars in modern agriculture highlights the importance of genetic diversity assessment. Therefore, a set of 96 rice genotypes collected from different parts of Manipur, India was used for genetic diversity assessment in the present investigation. Nine agronomic characters and 60 simple sequence repeat (SSR) microsatellite markers were the keys to differentiate their genetic relationship. A correlation study reveals the positive relationship of plant tiller number with yield which can be used as a selection criterion for the improvement of yield. The SSR profile depicts the presence of 118 alleles in the rice genotypes studied. The STRUCTURE analysis could be able to group the 96 rice genotypes into two major clusters and further sub-clustering into four sub-clusters in Cluster-I while into three sub-clusters in Cluster-II. Analysis of molecular variance (AMOVA) resulted in more variation in within individuals than among individuals and less variation exists among populations. A marker-trait association analysis identified 31 SSR markers significantly associated with eight yield-related traits. These markers would be useful for the identification of novel genes/alleles and could be deployed as a key indicator of selection for a marker-assisted breeding program of rice.