Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics

Capsicum chinense Jacq., one of the five domesticated species of pepper grown in the New World, is a major contributor to both local and international markets and the economy of the Caribbean islands. The planning and implementation of germplasm conservation and breeding programs for the sustainable use of C. chinense genetic resources are hampered by the poor understanding of the genetic structure and diversity of C. chinense in the region. In the present study, the genetic structure, diversity and relatedness of C. chinense germplasm collections within the Caribbean basin and South America were assessed using nuclear microsatellite markers. C. chinense accessions (102) representing seven geographical regions were genotyped using nine polymorphic nuclear microsatellite markers along with 16 accessions representing four other species of Capsicum. The results revealed that the highest genetic diversity (He = 0.58) was found in the Amazon region supporting the postulated center of diversity of C. chinense as the Amazon basin. The cluster analysis resulted in two distinct genetic clusters corresponding to Upper Amazon and Lower Amazon regions, suggesting two independent domestication events or two putative centers of diversity in these regions respectively. The cluster analysis further revealed that populations in Central America and the Caribbean may have been primarily derived from progenitors from Upper Amazon region and later diverged through geographical isolation. Conservation and germplasm collection programs should therefore target these genetically distinct clusters and satellite populations, towards supporting breeding programs to harness heterosis.