Molecular Characterization of Rice Accessions Using Microsatellite Markers

Genetic improvement mainly depends on the extent of genetic variability present in the population. The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. The objective of this study was to evaluate the genetic divergence of 24 rice accessions using SSR markers. A total of 48 alleles were detected in 24 accessions and the number of alleles per locus ranged from 1 to 5 with an average of 2 alleles per locus. The results revealed that out of twenty four, fourteen primers showed distinct polymorphism. The PIC value ranged from 0.07 to 0.79 with an average of 0.23. Markers having polymorphic reaction along with high PIC value i.e. RM 287 (0.79) and RM 22565 (0.69) should be potentially used for molecular characterization of accessions from various sources. The dendrogram based on SSR marker analysis grouped the rice accession into three clusters, where cluster II was the largest with 15 accessions. The cluster analysis showed higher level of genetic variation among the genotypes. Similarity coefficients ranged from 0.53 to 0.92. Coefficient of similarity revealed that the rice accessions of cluster I viz., Kala jira and CGR: 7144; Jhingo of cluster II and Cross 116 of cluster III were genetically distant from rest of the accessions as shown by low genetical similarity coefficient. With the aid of microsatellite makers and clustering data, different distantly related rice genotypes may be combined by intercrossing genotypes from different clusters to get hybrid varieties to get better heterosis. The information obtained from the DNA fingerprinting studies helps to distinctly identify and characterize the various genotypes.