Molecular diversity in rice genotypes differing in physiological mechanisms of salt tolerance through SSR and ISSR markers.

ABSTRACT

Two different DNA-based techniques viz, simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 20 rice genotypes possessing different physiological mechanisms contributing to salt tolerance. A total of 11 clear and repeatable bands were amplified from ten selected SSR primers pairs and 43 fragments were detected from nine ISSR primers. The level of polymorphism was 1.1% with SSR compared to 90.7% with ISSRs. Mean genetic similarity of 0.88 based on SSRs and 0.85 using ISSRs was observed. A total of 43 (39 polymorphic) and 11 bands were detected using 9 ISSR primers and 10 well distributed mapped SSR markers, respectively. Estimates of genetic similarity of ISSRs based on the 39 polymorphic markers between 20 rice cultivars ranged from 0.55 for PR108/CSR19 to 0.94 for Pokkali/CSR20 with an average of 0.81. The estimates revealed by the 11 polymorphic SSR bands showed the average value (0.94) and also the range of genetic similarity (from 0.86 to 1.00 for CSR22/CSR18 and CSR24/CSR20, respectively) reflecting their hyper variability and their high resolution power. The findings are likely to expedite breeding new salt tolerant cultivars by involving parents from diverse molecular clusters.