Diversity and haplotypes of rice genotypes for seedling stage salinity tolerance analyzed through morpho-physiological and SSR markers

Rice is sensitive to salinity at seedling and reproductive stages. A wide genetic variation was reported in rice for salinity tolerance, a pre-requisite for any plant breeding programme. In the present study, we have characterized a set of 192 rice genotypes for their seedling stage salinity tolerance by combining morpho-physiological and molecular markers. The experiment was conducted under control (EC ∼ 1.2 dS m−1) and saline stress conditions (EC ∼ 12 dS m−1) using hydroponics. There was a significant difference among the genotypes for the ten characters studied. Under saline conditions, the chlorophyll concentration, root length, shoot length, and K+ concentration decreased as compared to control condition and the opposite was true for Na+ concentration. Na+ concentration showed strong negative correlation with chlorophyll concentration, K+ concentration, root length and shoot length. Thirteen SSR markers associated with Saltol region on chromosome 1 were screened across the 192 rice genotypes, of which ten gave scoreable results. Polymorphism Information Content (PIC) and genetic diversity indices showed that the markers RM 493 and RM 10793 were highly useful for distinguishing genotypes. Hierarchical cluster analysis revealed eleven clusters for phenotypic and genotypic data, but very low correspondence was observed between two dendrograms. The haplotypes of genotypes for Saltol associated markers, when compared with FL 478, revealed that the genotypes CST 7-1 and Arvattelu could be good candidates for novel genomic regions governing salinity tolerance in rice.