Studies on genetic diversity among rice genotypes using RAPD and SSR markers

The genetic variation and relationships among 20 rice genotypes were evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. A high level of polymorphism were found with both RAPD and SSR markers and the mean polymorphism information content (PIC) values were 0.467 and 0.495 for RAPD and SSR markers, respectively. In RAPD analyses, 81 out of 94 bands (86.17%) were polymorphic. The number of alleles ranged from 3 to 7 per primer, with an average of 4.6 per primer. Cluster analysis based on RAPD banding pattern grouped the rice accessions into 2 major clusters. It also showed that N22 was distantly related to NDR18 with the Jaccard's coefficient of 0.63. Cluster analysis based on microsatellite data confirmed this clustering pattern of the accessions. SSR analysis also revealed that N22 was distantly related to Taraori with the Jaccard's similarity coefficient of 0.69. Combined dendrogram analysis showed that N22 was distantly related to Sahay Pasand with Jaccard's coefficient of 0.63. The two marker systems contrasted most notably in pair-by-pair comparisons of relationships. SSR analysis resulted in a more definitive separation of clusters of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination of relationships between accessions that are too close to be accurately differentiated by RAPD markers.