Salt stress responsive genetic polymorphism analysis among promising rice genotypes using microsatellite markers

Abstract

Using a panel of six salt stress response related microsatellite primer pairs, the molecular level polymorphism was examined amongst sixteen rice genotypes. Altogether 49 allelic variants including 30 shared and 19 unique alleles were detected with an average of 8.16 alleles per primer pair. 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 493 and RM10772 had relatively greater polymorphism information content. Considering the number of alleles, polymorphism per cent and polymorphism information content along with gene diversity as the basis, RM 10772 appeared to be comparatively most polymorphic and informative primer for the purpose of salt stress response related discrimination of entries. Ample genetic variability revealed by the analysis of amplification profiles based differentiation and divergence pattern conveniently allowed unambiguous discrimination and classification of the tolerant and susceptible entries. Similarity coefficients based hierarchical classification pattern was completely validated by the principal coordinate analysis based spatial distribution of the genetic profiles of sixteen genotypes. Neighbor joining tree based on six salt stress responsive microsatellite primers dependent similarity indices also discriminated the susceptible and tolerant entries. Precise analysis of the genetic polymorphism indicated that the improvement in salt tolerance can be achieved by selecting parental genotypes from different clusters for combining different salt tolerance components into a single genetic background. Presence of ample genetic variability, as revealed by salt stress response related microsatellite primer pairs, signified the prospects for developing highly salt tolerant rice varieties through a combination of superior alleles of genes controlling salt tolerance in different genotypes.