Genome-wide assessment of genetic diversity and population structure of Capsicum in Southwestern Colombia using DArTseq markers

Chili peppers ( Capsicum spp.) are among the most widely cultivated horticultural crops worldwide due to the high demand for their pungent fruits. Despite Colombia’s high diversity of Capsicum species and varieties, its genetic resources remain underrepresented in international markets and scientific studies. This study aims to characterize the genetic diversity and population structure of Capsicum accessions from southwestern Colombia. Accessions were collected through field surveys in local markets and protected natural areas and genotyped using DArTseq platform. A total of 69 accessions representing seven species were genotyped using 3681 high quality DArT-SNP markers. Standard genetic diversity metrics and population structure analyses were performed. The analysis revealed low observed heterozygosity (mean 1%) and high inbreeding coefficients (F IS : 0.24). However, expected heterozygosity values indicate that these accessions still retain substantial genetic variability, highlighting their potential for breeding and genetic improvement programs. Population structure analysis revealed clear genetic differentiation between Andean and domesticated Capsicum species. Moreover, Silico-DArT markers could discriminate between wild and domesticated accessions within C . annuum and C . frutescens . This study represents the first genome wide assessments of Andean Capsicum species using DArTseq genotyping. These findings contribute to the understanding and conservation of Capsicum genetic resources of Southwestern Colombian and provide valuable information for future breeding programs.