Exploring the origin and diversification of the locoto chile (Capsicum pubescens): Multiple approaches using RAD-seq data

Abstract

Capsicum pubescens is a well-known hot chile from South American Andean highlands, nowadays cultivated from NW Argentina to Central America. The species is known only as a cultigen and not in wild form. The origin of C. pubescens has been puzzling while the knowledge of its evolutionary history and genetic diversity is scarce. A couple of wild Andean species have been proposed as its closest allies and/or putative ancestors, with which C. pubescens can interbreed. However, crossing experiments and DNA data analyses have produced some contradictory results, being C. pubescens resolved into an isolated clade.The RAD-sequencing approach was thus followed to analyze C. pubescens origin and affinities, diversification and genetic structure by using genome-wide data. The phylogenetic affinities of C. pubescens were strongly resolved, being a sister species to those considered its closest allies, but it is ascertained that none extant Capsicum species would be its wild ancestor. Within C. pubescens, two major genetic groups can be recognized: 1) individuals from Bolivia and Argentina and, 2) individuals from Peru, Ecuador and Central America, including Mexico. Based on phylogenetic reconstructions, C. pubescens area of origin could be located in the central-western Bolivian highlands. This would be in concordance with the wide morphological variation of the species in that region (i.e. flowers, fruits, pubescence, etc.). Overall, the current results allow deepening the knowledge of the affinities and distribution of the genetic diversity of the locoto chile, offering new ideas, supported by genome-wide data, about its origin and expansion.