Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering

Abstract

The hot chile Capsicum pubescens is mainly cultivated in Central-South America's mid-highlands, from Mexico to northwest Argentina. Despite being a crop of economic and cultural importance, little is known about its evolution and the genetic diversity and structure it harbors. Thus, RAD-sequencing technology was applied to generate genomic single nucleotide polymorphism (SNP) data from 67 samples of locoto chile cultigens from different Latin American countries, to characterize the diversity and genomic structure of the species throughout its range of distribution/cultivation. After applying various information content and quality filters, 1462 SNPs (out of 183569) were retained and used for population inferences. Three geographically structured main groups were distinguished, associated with a North-South distribution pattern: G1) cultigens from Central America to Mexico, G2) from Ecuador, Peru, to central-western Bolivia, G3) from central-southern Bolivia to Argentina. The AMOVA showed a moderate degree of divergence between the inferred clusters, while the pairwise FST values were consistent in showing a correlation between genetic and geographic distance. A high level of admixture/shared ancestry was also detected, mainly in G2 that presented higher genetic diversity. Indeed, G2 includes individuals from La Paz (Bolivia) surroundings with a broad morphological variation, including the smallest and fleshiest fruits, which suggests that new and extensive expeditions in central-western Bolivian highlands are needed to gain a better understanding of C. pubescens origin and diversification. Overall, this study provides new genome-wide supported insights into the diversity and differentiation of the locoto chile and will be useful for conservation and management strategies.