A panel of six salt stress response related microsatellite primer pairs was utilized to examine the molecular level polymorphism for molecular characterization and elucidation of the nature and extent of differentiation and divergence of sixteen rice genotypes. Polymorphism at the genotypic level was recognized on the basis of presence or absence of bands, besides variation in number and position of bands amongst genotypes. Altogether 49 allelic variants were detected at 8 loci with an average of 6.12 alleles per locus. Considerably greater polymorphism per cent was recorded for the primer pairs RM 140, RM 10764, RM 10772 and RM 10864. Amongst primer pairs utilized in the present study, RM 140, RM 10665, RM 10772 and RM 10864 had relatively greater polymorphism information content. Considering the number of alleles and polymorphism per cent, in conjunction with polymorphism information content, RM 10772 appeared to be the most polymorphic and comparatively more informative primer for the purpose of salt stress response related discrimination of entries under evaluation. Ample genetic variability revealed by the analysis of differentiation and divergence pattern based on amplification profiles allowed unambiguous discrimination and classification of the entries. Inference derived from the results of the similarity coefficients based approach was completely supported by the principal coordinate analysis of the genetic profiles from sixteen genotypes. The results indicated that the improvement in salt tolerance can be achieved by selecting parental genotypes from different clusters with apparently diverse salt tolerance mechanisms for combining different salt tolerance components into a genotype. Existence of ample genetic variability revealed by salt stress responsive microsatellite primer pairs signified the prospects for developing highly salt tolerant rice varieties through combining superior alleles of genes controlling salt tolerance in different genotypes. 

Key Words: Cluster analysis, Genetic variability, Genetic similarity, Genetic polymorphism, Microsatellite, Rice, Salt tolerance