Hot pepper (Capsicum annuum) is the most important spice crop belonging to the Solanaceae family. Despite its economic importance, little research has been undertaken on genetic diversity of hot pepper germplasm and cultivars in Ethiopia. The aim of this study was to investigate the genetic diversity among the Ethiopian hot pepper germplasm collections using ISSR markers. Genetic diversity of 53 hot pepper (Capsicum annuum) Germplasm collections and cultivars was studied using ISSR markers at plant Genetics research Laboratory of Addis Ababa University, Ethiopia. Genomic DNA was extracted from 53 accessions of individuals using CTAB extraction method. A diluted genomic DNA was subjected to PCR amplification. Two di-nucleotide and two penta nucleotide repeat primers amplified a total of 29 clear and reproducible bands. All bands were 100% polymorphic. Both UPGMA dendrogram and neighbor joining (NJ) trees were constructed for the individual cultivars using Jaccard’s similarity coefficient. The dendrogram clearly indicated two major clusters and three sub-clusters. The genetic diversity among C. annuum populations and cultivar groups considered in the present study indicated that Mirab Gojjam population exhibited a genetic diversity of 0.31 and Shannon diversity index of 0.47, while the Gurage, Kembata, Bale and Semen Gondar population of C. annuum showed 0.26, 0.22, 0.12 and 0.11 for genetic diversity and 0.39, 0.33, 0.19 and 0.17 Shannon diversity index values respectively. Generally Mirab Gojjam population showed higher genetic diversity but Semen Gondar population showed least genetic diversity. Furthermore Analysis of molecular variance (AMOVA) demonstrated highly significant (p=0.0) genetic diversity within populations (55.3%) than among populations (44.7%). Generally, on the basis of bands generated by all primers, ISSR revealed high levels of genetic diversity within and among population of Ethiopian C. annuum. Further study of ISSR using more geographic area coverage and primers is recommended to obtain confirmative results.
Keywords: C. annuum, Genetic diversity, Genomic DNA, ISSR marker, Polymorphism