Genetic diversity in cultivars and landraces of rice as revealed by SSR markers

Rice yields have now apparently reached a plateau possibly due to use of common dwarfing gene sources and alleles contributing yield potential that has led to narrowing genetic base of these high yielding cultivars. Therefore, the use of local germplasm calls for its evaluation and characterization before embarking on their use in a systematic breeding programme. In the present study 40 SSR primers generated a total of 250 alleles across these genotypes with a range of 2 - 11 alleles per locus and a mean of 6.89 alleles per locus. The PIC values, measuring allelic diversity and polymorphism ranged from 0.490 (RM2592) on chromosome-1 to 0.806 (RM585) on the chromosome-6, with a mean PIC value of 0.719 per locus. Similarity coefficients (measuring relatedness) were used to construct the dendogram and clustering pattern. Pairwise similarity coefficients ranged from 0.10 to 0.89, with the average similarity coefficient around 0.40. Similarity coefficient value revealed presence of good genetic diversity among these genotypes at the molecular level. Clustering pattern revealed grouping of these genotypes into 5 clusters. All the landraces got grouped into 2 clusters viz. cluster-I (13) and cluster-II (7) except Rehman Batt-1 which got grouped in the cluster-III which mostly contained genotypes for higher altitude conditions. High yielding varieties for valley basin conditions formed cluster-V (5 cultivars), while cluster-IV contained cutivars mostly of K-series.