Using a set of five salt stress responsive microsatellite primer pairs, simple sequence length polymorphism was examined in twelve genotypes of rice in order to characterize these genotypes and to examine the nature and the extent of differentiation and divergence among them at the molecular level. Additionally, the primer pairs were evaluated for their polymorphism information content for identification of polymorphic and informative markers. Utilizing these primer pairs, amplification was successfully achieved and polymorphism was recognized on the basis of presence or absence of bands, besides variation in number and position of bands. Altogether 38 allelic variants were detected at 7 loci with an average of 5.42 alleles per locus. The primer pairs RM 204 and RM 242 generated considerably greater percentage of unique alleles in conjunction with higher level of polymorphism and appeared to be highly polymorphic and comparatively more informative primers for the purpose of molecular characterization of entries under evaluation. An analysis of differentiation and divergence pattern based on amplification profiles obtained with salt stress responsive microsatellite primer pairs revealed ample genetic variability and allowed unambiguous discrimination and classification of the genotypes. The results indicated that the improvement in salt tolerance can be achieved by selecting parental genotypes prior to intercrossing based on microsatellite markers and different salt tolerance components can be combined into a genotype by intercrossing genotypes from microsatellite markers based different clusters with diverse salt tolerance mechanisms.  

Key words: Genetic similarity, Genetic variability, Microsatellite, Rice, Salt tolerance