Analysis of pepper genetic diversity and genetic relationship is important in selecting genetically diverse parental lines drawn from several genetic populations, and also helps to implement effective conservation strategies. For this purpose, 25 pepper genotypes comprising both accessions and improved varieties were examined using 16 SSR markers. The markers were polymorphic and showed a mean PIC value of 52% with a range of 8 to 80%, and generated a total of 67 alleles, with an average of 4.19 alleles per marker. The gene diversity ranged from 0.09 to 0.82, with an average of 0.57. Interestingly, pairwise genetic dissimilarity was the highest (1.00) between PBC-731 and Acc-22, and the lowest (0.25) between Acc-13 and Acc-11 genotypes. This is expected because improved varieties are genetically far from accessions than accessions are from each other. Neighbor-joining (NJ) tree produced three major clusters consisting of C1=100% accessions, C2= 67% improved varieties, and 33% accessions, whereas C3= 50% accessions and 50% improved varieties. The principal coordinate analysis (PCoA), showed a scatter plot with a wide dispersion of the genotypes in all the quadrants without forming a clear cluster, and some genotypes like PBC-731, Acc-45, Acc-9, and Acc-22 are plotted far from the central axis. The population structure generated an optimal groups of ΔK=4 with a high level of admixtures. The analysis of molecular variance (AMOVA) both based on STRUCTURE results and grouping into the accessions and improved varieties partitioned the total variance into 9% among groups, and 91% among individuals in the groups. The high level of genetic diversity found in Ethiopian pepper genotypes in the present study will help breeders to utilize the genotypes for further improvements in pepper germplasm.
Key words: Capsicum annum, genetic diversity, hybridization, pepper, SSR markers.