Genetic Structure and Phylogenetic Relationships of Capsicum chinense

Abstract

<jats:p><jats:italic>Capsicum chinense</jats:italic> 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 <jats:italic>Capsicum annuum</jats:italic>, which is the most commercially exploited domesticated species internationally, <jats:italic>C. chinense</jats:italic> has not been methodically collected or characterized for systematic improvement through plant breeding. The objectives of the study were to assess the diversity of <jats:italic>C. chinense</jats:italic> and its structure within the Caribbean basin and to determine its phylogenetic relationship to groups within South America. DNA isolated from 201 accessions of <jats:italic>C. chinense</jats:italic>, 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 <jats:italic>C. chinense</jats:italic> (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 <jats:italic>C. chinense.</jats:italic> 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 <jats:italic>C. chinense</jats:italic> may have potential for exploiting heterosis in breeding. The implications of the findings to the understanding of the phylogenetic origin and distribution of <jats:italic>C. chinense</jats:italic> are discussed.</jats:p>

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

“…The FCAbased clustering largely grouped the C. baccatum accessions as a function of their geographic origin, establishing three well-defined groups for Ecuador, Peru, and Bolivia. These results are in agreement with those obtained by Moses and Umaharan (2012) and Moses et al (2014), who proposed the existence of three distinct phylogeographic gene pools in C. chinense: one from the upper Amazon region (Peru, Ecuador, and Bolivia), one from the lower Amazon region (Brazil and the Guianas), and another from the Caribbean region. Cultivated C. baccatum is not commonly distributed outside South America, and the commercial value of this species is mainly confined to regions of this subcontinent (Djian-Caporalino et al, 2007); thus, the possibilities to incorporate accessions from different regions were limited.…”

Plant and fruit trait variations among four Capsicum species in a Caribbean germplasm collection

“…In the genetic diversity study conducted on a subset of this germplasm collection (Moses and Umaharan, 2012), three distinct phylogenetic clusters were identified (A -C); the largest cluster (B) contained most accessions from the Upper Amazon, Central America, the Southern Caribbean and the Guianas including Venezuela (collectively referred to as the Guiana Shield in the present study). A minority of the Lower Amazon accessions was included in this cluster B.…”

“…As proposed by Moses and Umaharan (2012), the physical barrier between the Upper and Lower Amazon regions has possibly been quite effective in preventing the movement and exchange of germplasm between these two regions.…”

“…Additional regions of diversity can also be found in the Caribbean (Moses and Umaharan, 2012). Current estimates of wild species of Capsicum exceed 30, of which only five are domesticated (Moscone et al, 2007): C. annuum L.; C. frutescens L.; C. chinense Jacq.…”

“…Genetic diversity studies have recently reported on a subset of collection (Moses and Umaharan, 2012); however, there is limited morphological information on plant and fruit traits.…”