RAPD and SSR based DNA Fingerprinting and diversity analysis in riice (Oryza Sativa L.)

Abstract

The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. The objective of this study was to evaluate the genetic diversity of 20 varities/genotypes of rice(Oryza sativa) using the random amplified polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). In RAPD Analysis twenty primers was generate a total of 116 RAPD of which 112 were polymorphic. The number of amplification products produced by each primer varied from 4 to 7 with an, average of 5.8 bands primer. Genetic diversity of 20 cultivars estimated by polymorphic information content (PIC) value ranged from0.334 to 0.886 with average of 0.614 in RAPD analysis. The cluster dendrogram of RAPD revealed 2 major clusters and Cluster II was the largest and included 14 genotypes while clusters I comprising 6 genotypes. According to dendrogram Apo was distantly related to Rajeshwari with coefficient 0.317. Twenty SSR primers generated a total of 66 alleles with an average 3.3 alleles per primer. Genetic diversity of 20 cultivars estimated by polymorphic information content (PIC) value ranged from 0.00 to 0.977 with an average of 0.670 in SSR analysis. The cluster dendrogram of SSR revealed 3 major clusters consist of another 4 major subgroups. Cluster II was the largest and included 17 genotypes while clusters 1 comprising only 2 genotypes. According to dendrogram genotype Apo was distantly located with Rajeshwari with similarity coefficient 0.591. The cluster dendrogram of combined analysis revealed 2 major clusters. Cluster II was the largest and included 14 genotypes while clusters I comprising 6 genotypes and Apo was distantly located with Udaya with similarity coefficient 0.561. Conclusion of this studies that SSR more useful as compare to RAPD because SSR show high PIC value. The information generated from these studies can be used in the future of rice(Oryza sativa) breeding programs.