Diversity studies are an essential step in plant breeding and understanding the genetic relationships between pepper accessions may provide an effective management tool for their conservation, as well as help inform plant breeding efforts. The objective of the study was to assess the diversity and structure of pepper germplasm grown in Eritrean to help inform improvement programs. Local pepper ( Capsicum spp .) germplasm collected from farmers and institutions in Eritrea was assessed using 16 quantitative morphological traits. The evaluation was conducted in two sites using a Randomized Complete Block Design with three replications. The data from the two sites were subjected to Principal Component Analysis, Hierarchal clustering with Euclidean distance and Analysis of variance. Cluster analysis of the combined data grouped the 60 genotypes into five clusters and 10 sub-clusters confirming the diversity of the collection that can be useful for selection and source of desired genes. A selection index was used to identify at least four promising genotypes (HD0134, HD0031 and NRSG21 and NRSAF06) for dry consumption purposes. The results of the current study revealed the relatively high level diversity existed within the evaluated collections and partitioned them into meaningful groups.
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