Detection of DNA polymorphism among rice landraces and cultivars using STMS and RAPD markers

Characterization and quantification of genetic diversity has long been a major area of research in evolutionary biology. Information on the genetic diversity within and among related crop varieties and elite genotypes are essential for further exploitation of plant genetic resources. It contributes in quantifying variation in germplasm as well as predicting potential genetic gains. STMS (SSR) markersbeing highly polymorphic, abundant andeasy to use have become the marker of choice for diversity analysis while RAPD primers are also popular due to their dominant character. Further, they are abundant, easy to handle, less costly and detect huge polymorphism in the genome. Therefore, using both of these marker systems, ample genetic variation available in rice germplasm can be exploited to predict potential genetic gains. In the present study, six rice genotypes that included three landraces (viz. Thakurbhog, Karahani and Kalanamak) and three popular cultivars (viz. Pusa Basmati 1, Ketakijoha and Narendra Usar-3) have been studied tounderstand allelic variability using RAPD and STMS. A total of 10 rice specific STMS primers and 22 RAPD primers were used for the study. STMS primers revealed polymorphism (100%) with amplification of product varied from 50 to 1200 bp between landraces and cultivars and number of alleles ranged from 1 to 3 with an average of 1.9 alleles per primer. The Polymorphic information content (PIC) of STMS primers among landraces and cultivars varies from 0.50 to 0.97 with average of 0.72. RAPD primers on the other hand, revealed sufficient polymorphism (95%) with ampliconproduct variation rangedbetween 0.3 to 3 kb and number of alleles per primer ranged from 2 to 4 with an average of 2.8. The Polymorphic information content (PIC) of RAPD varied between 0 to 0.48 (average 0.14/marker). Ample polymorphism has been observed in both the marker system and both can be used individually towards assessing genetic variability among the cultivars. Moreover, when the marker system was compared, they were found to be competent and comparable.