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

Abstract

Several attempts in recent decades have been devoted to investigating the genetic and phenotypic diversity harbored by the genus Capsicum. Particular efforts have been directed to old varieties or landraces. However, the genus is still under‐researched, and further investigations that accurately define the relationships among species and identify those geographic regions with greater variability are required. In the present work, 107 Capsicum landraces from Ecuador, Peru, and Bolivia were evaluated with a set of 16 microsatellite markers. In total, 187 alleles were detected in the Andean collection, and 49.7% of those were recorded as unique alleles. Indices of genetic diversity were high and very similar in the three evaluated countries, although the domesticated Capsicum species carrying the highest diversity varied among them: C. frutescens (L.) in Ecuador, C. chinense (Jacq.) in Peru, and C. annuum (L.) in Bolivia. Comparison of Andean accessions with others coming from diverse origins revealed intraspecific genetic differentiation in C. annuum, C. chinense, C. frutescens, C. baccatum (L.), and C. pubescens (Ruiz et Pav.), following a geographic pattern. Similarly, assessment of the genetic diversity currently maintained in Ecuadorian Capsicum species brought to light a dramatic decrease in the genetic variability of cultivated peppers when compared with those harbored by old landraces. Analysis of genetic relationships among Capsicum species was in agreement with previous taxonomic classifications: C. annuum, C. chinense, and C. frutescens were clustered as independent and highly related species; C. cardenasii (Heiser et Smith) and C. eximium (Hunz.) were indistinguishable as a single species; and C. chacoense (Hunz.) was placed between C. pubescens and C. annuum complexes.