Pangenomic and Phenotypic Characterization of Colombian Capsicum Germplasm Reveals the Genetic Basis of Fruit Quality Traits

Capsicum is one of the most economically significant vegetable crops worldwide, owing to its high content of bioactive compounds with nutritional, pharmacological, and industrial relevance. However, research has focused on C. annuum, often disregarding local diversity and secondary gene pools, which may contain hidden variation for quality traits. Therefore, this study evaluated the genetic and phenotypic diversity of 283 accessions from the Colombian germplasm collection in the agrobiodiversity hotspot of northwest South America, representing all five domesticated species of the genus. A total of 18 morphological, physicochemical, and biochemical fruit traits were assessed, including texture, color, capsaicinoid, and carotenoid content. The phenotypic data were integrated with genomic information obtained through genotyping-by-sequencing (GBS) using the C. annuum reference genome and a multispecies pangenome. Fixed-and-Random-Model-Circulating-Probability-Unification (FarmCPU) and Bayesian-information-and-Linkage-disequilibrium-Iteratively-Nested-Keyway (BLINK) genome-wide association studies (GWAS) were performed on both alignments, respectively, leading to the identification of complex polygenic architectures with 144 and 150 single nucleotide polymorphisms (SNPs) significantly associated with key fruit quality traits. Candidate genes involved in capsaicinoid biosynthesis were identified within associated genomic regions, terpenoid and sterol pathways, and cell wall modifiers. These findings highlight the potential of integrating pangenomic resources with multi-omics approaches to accelerate Capsicum improvement programs and facilitate the development of cultivars with enhanced quality traits and increased agro-industrial value.