J Plant Mol Breed (2017) 5(2): 27-37 DOI: 10.22058/JPMB.2019.91684.1169 RESEARCH ARTICLE --------------------------------------------------------------------------------- *Corresponding author (): shifeey@gmail.com Received: 10 Aug. 2018/ Revised: 12 Sept. 2018 Accepted: 11 May 2019 Genetic diversity study of Ethiopian hot pepper cultivars (Capsicum spp.) using Inter Simple Sequence Repeat (ISSR) marker Alayachew Shiferaw Alemu*, Atnafu Destaw Mullualem, Gedefa Samuel Adugna Applied Biology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia ABSTRACT: Hot pepper (Capsicum spp.) is an economically important spice widely cultivated and consumed in Ethiopia. In spite of its wide importance, there is no information available on the molecular genetic diversity of this crop. Cultivars characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programs. Using five ISSR primers, a total of 37 scorable bands were generated of which 35 (94.6%) were polymorphic bands. The diversity of polymorphic bands within population ranged from 51.35% to 91.89 % with a mean of 66.6 %, Nei’s genetic diversity of 0.19 - 0.30 with a mean of 0.28, and Shannon information index of 0.29 - 0.45 with a mean of 0.43. With all diversity parameters, the highest diversity was obtained from amhara2 populations, whilst the lowest was from Oromia2. From Jaccard’s pairwise similarity coefficient, Oromia1 and oromia2 were the most related populations exhibiting 0.956 similarity and Semn omo and Amhara 2 were the most distantly related populations with similarity of 0.827. Clustering was showed that there is strong correlation between geographic distance and genetic diversity of Ethiopian hot peppers cultivars because geographically closely related species have been clustered together. Amhara 2 populations exhibited the highest genetic diversity so that the populations should be considered as the primary sites in designing conservation areas for this crop in Ethiopia. Further, it is suggested that molecular markers are valid tags for the assessment of genetic diversity in Capsicum spp. cultivars. KEYWORDS: Capsicum, Cultivars, Cluster analysis, Diversity, Pepper INTRODUCTION Hot pepper (Capsicum spp.) commonly known as red pepper or chili pepper is a dicotyledonous flowering plant which belongs to the family of Solanaceae [18]. It is an important commercial crop cultivated exclusively in tropical and temperate zones of the world and grown on more than 1.5 million hectares worldwide [11]. Peppers are usually classified based on fruit characteristic, including pungency, color, shape, flavor, size and use [3- 5]. Pepper cultivars are grown in Ethiopia mainly in South Nation and Nationalities of Peoples (SNNP), since its introduction in the early 17th century by the Portuguese [14]. Capsicum annum is the main types of capsicum species that has grown in the country. Pepper species are grown at a medium altitude of 1,400 to 2,120 meters above sea level. In Ethiopia, it is grown under rain fed conditions in areas with 600-1,250 mm of annual rain. Hot pepper covers 67.98% of all the area under vegetables in Ethiopia. South Nations, Nationalities and Peoples Regional State (SNNPS) contribute a significant portion to the country’s total pepper production [6]. It is the main part in the daily diet of most Ethiopian societies. The average daily consumption of hot pepper by