Genetic diversity studies in pepper (Capsicum spp)

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Genetic characterization using morphological and molecular markers is imperative in making available useful information on the genetic diversity within a species. Such information is vital in providing the basis for proper conservation strategies and to orientate effective breeding methods. The overall objective of this study was to examine the genetic diversity and relatedness among in-country pepper accessions. Fifty local pepper genotypes were characterized using 35 quantitative and qualitative traits from seedling emergence to crop maturity. Morphological data were subjected to principal component analysis (PCA) followed by hierarchical cluster analysis using euclidean similarity coefficient. The first four principal components accounted for 72.44% of the total genetic variance among the 50 pepper genotypes with the larger part of the variance explained by cotyledon leaf width, fruit width, plant height and fruit length. The study showed a great variation in fruit traits revealing six fruit shapes and four fruit colours. Although there was substantial variation among the accessions based on phenotypic traits, cluster analysis revealed low genetic diversity among the accessions. Molecular analysis using 8 SSR markers generated a total of 35 alleles with an average of 4.38 alleles per locus. Polymorphism information content (PIC) ranged from 0.20 to 0.74 with an average of 0.42. The mean values of gene diversity and heterozygosity were 0.44 and 0.26 respectively , signifying a substantial amount of polymorphism among the primers. Molecular cluster analysis based on UPGMA revealed a much wider genetic dissimilarity of 0.26 to 0.90. The accessions were clustered into two main groups at 0.26 with cluster 2 having fifteen sub-clusters at a similarity coefficient of 0.46. The study has shown that both morphological and SSR markers are effective tools in studying genetic diversity in Capsicum species. This observed diversity among the pepper genotypes can therefore be used for improving pepper through selection and hybridization.
A thesis submitted to the Department of Crop and Soil Sciences, Faculty of Agriculture, KNUST, Kumasi in partial fulfillment of the requirements for the degree of Master of Science, 2013