Development of informative SNP markers for Capsicum species identification using phenotypic and genomic data

Abstract

Accurate identification of Capsicum species is essential for effective germplasm conservation, breeding, and taxonomic research. However, traditional classification based on morphological traits is often complicated by overlapping features and interspecific hybridization. In this study, 316 Capsicum accessions representing five species were analyzed, revealing distinct, species-specific corolla color patterns. Although corolla color was initially considered for genome-wide association studies (GWAS), strong population structure caused by species differentiation confounded interpretation of trait-locus associations. Instead, phenotypic traits and genome-wide nucleotide variation were leveraged to identify a subset of informative single nucleotide polymorphisms (SNPs) useful for species discrimination. From an initial pool of 82 candidate SNPs, four were selected based on discriminatory power and allele distribution, while two additional markers were incorporated from broader variant data to enhance classification accuracy. The resulting six-marker panel demonstrated high performance in an independent validation set of 333 accessions, achieving 95.6 to 100 percent accuracy, sensitivity, and specificity across species. Phylogenetic clustering using the selected SNPs corresponded closely with known taxonomic relationships. Furthermore, the markers successfully classified 50 previously unassigned accessions. These SNPs provide a reliable and cost-effective molecular tool for Capsicum species identification, with practical applications in germplasm management at gene banks and in breeding programs.