Genetic Structure and Phylogenetic Relationships of Capsicum chinense

Capsicum chinense is commercially the most important pepper species grown in the Caribbean. It is popularly used to impart pungency and flavor to Caribbean cuisine. However, unlike Capsicum annuum, which is the most commercially exploited domesticated species internationally, C. chinense has not been methodically collected or characterized for systematic improvement through plant breeding. The objectives of the study were to assess the diversity of C. chinense and its structure within the Caribbean basin and to determine its phylogenetic relationship to groups within South America. DNA isolated from 201 accessions of C. chinense, representing geographical regions where the species is found, were amplified using arbitrary primers to generate 138 polymorphic and reproducible random amplification of polymorphic DNA (RAPD) markers. Nei's and Shannon's diversity indices for C. chinense (0.28 and 0.419, respectively) were higher in South America compared with Central America or the Caribbean, corresponding to its putative center of diversity. The study showed the existence of three phylogenetic clusters within C. chinense. The largest cluster consisted of accessions from the Upper Amazon region, the Guianas including Venezuela, and the Lesser Antilles of the Caribbean. The other major cluster was represented by accessions principally from the Lower Amazon region. Another distinct but small cluster consisted of samples solely from the Greater Antilles of the Caribbean. The discovery of the three phylogenetic clusters within C. chinense may have potential for exploiting heterosis in breeding. The implications of the findings to the understanding of the phylogenetic origin and distribution of C. chinense are discussed.