Genetic Diversity in Certain Genotypes of Chilli and Paprika as Revealed by RAPD and SSR Analysis

Genetic relationships between thirteen genotypes of chilli and paprika collected from different places of India were analyzed using twelve RAPD and nine SSR primers. Clustering based on the generated markers was conducted using NTSYS software’s. The RAPD primers produced a total of 78 bands of which 65 were polymorphic with a mean of 5.41 polymorphic bands per primer while the SSR primers produced 28 SSR loci with a mean of 3.22 alleles per SSR locus. The similarity index matrix ranged from 0.36 to 0.91 (RAPD) and 0.117 to 0.9 (SSR) with mean of 0.62 and 0.39 respectively. Polymorphic Information Content (PIC) values of the SSR primers ranged from 0.00 to 0.75 with an average value of 0.546. The resulting RAPD and SSR dendrograms separated the cultivars with small and erect fruit position from the large and medium fruited cultivars with declining fruit position. Both RAPD and SSR markers showed genetic variability in the studied pepper genotypes and they are powerful tools for estimating genetic similarities and diversity.