Genome profiling of differential salt stress responsive landraces and varieties of rice using ISSR markers

Using 14 ISSR primers for molecular profiling in relation to salinity tolerance of 18 landraces and varieties of rice, altogether 483 allelic variants including 236 shared and 247 unique alleles were generated with an average of 34.50 alleles per primer, revealing ample genetic differentiation and divergence amongst the entries under evaluation. Every primer generated polymorphic amplified products, but only 12 out of 14 primers yielded unique products. The primers having (AG)8YT, (CT)8A, (AG)8YA, (GA)8YT, (GA)8YC, (CT)8G, (TC)8C, (GATA)4 and (GA)8YG repeat motifs recorded relatively higher polymorphism per cent expressed in terms of the percentage of unique alleles in descending order of magnitude. Polymorphism information content of the primers varied from 0.612 to 0.992 for the primers (GACA)4 and (AG)8YA, respectively, with an average of 0.919 across the primers. Comparatively higher numerical values were obtained in respect of the primers (GA)8C, (CT)8A, (CT)8G, (TC)8C, (TC)8G, (AG)8YT, (AG)8YA, (GA)8YT, (GA)8YC, (GA)8YG and (GATA)4 amongst all the primers, reflecting their greater allelic richness and diversity. Poly-GA containing anchored primers produced the highest number (44.8) of allelic variants per primer followed by poly-CT, poly-AG and poly-TC containing anchored primers. But, the highest mean polymorphism per cent, highlighting the proportion of unique alleles, was exhibited by poly-AG followed by poly-GA, poly-CT and poly-TC containing anchored primers Clustering based on only poly-GA and poly-AG containing anchored primers provided more efficient genotypic discrimination in relation to salt stress responsiveness of the rice varieties. Moreover, a panel of only three poly-AG containing anchored primers facilitated perfect discrimination of rice varieties in accordance with their responsiveness to salinity stress. These primers can be efficiently utilized as functional instruments for connecting genotypic and phenotypic differences in relation to salt stress responsiveness. Principal coordinate analysis completely supported the results obtained from hierarchical classification of the landraces and varieties.