Genetic Diversity in Popular Rice Varieties of India

The genetic diversity of 25 improved varieties and four traditional varieties were characterized using a set of 20 well chosen and polymorphic microsatellite (SSR) primer pairs. The SSR markers used were polymorphic (100.0%) and generated the reliable information about the relatedness of the varieties. High values of polymorphism obtained in the characterization were attributed to hypervariability of the microsatellite markers. Among the popular varieties, the mean genetic similarity of 0.38 was observed indicating the wide diversity of the popular varieties. Cluster analysis based on 87 SSR marker alleles grouped 29 genotypes into two major clusters. The first major cluster comprised 9 genotypes of traditional varieties and early improved varieties. The second major cluster consisted of 20 improved varieties of complex pedigree and several recombination events. Principal component analysis revealed four clusters, out of which one cluster included seven genotypes from rainfed shallow land ecology suggesting the grouping was based on physiological traits. Unique alleles were generated for 14 varieties, which can be used as molecular tags.