Genetic diversity analysis of pepper (Capsicum annuum L.) germplasm resources based on the phenotypic traits

Abstract Pepper ( Capsicum annuum L.) is a globally significant vegetable crop, with China accounting for one-third of the world's total pepper production. The genetic diversity of pepper germplasm resources is critical for further research and breeding efforts. In this study, 50 pepper accessions were sampled and analyzed to assess genetic diversity. A comprehensive analysis was conducted using the coefficient of variation, principal component analysis (PCA), and cluster analysis to evaluate the diversity and variation in 33 phenotypic traits across the accessions. Coefficient of variation for average fruit weight reached 102.91%, highlighting significant differences among the pepper accessions. Correlation analysis revealed a strong negative relationship between average fruit weight and both soluble solids content and ascorbic acid content. PCA indicated that the first three principal components explained 92.73% of the total variation, with key traits such as leaf color, fruit weight, and fruit color being most influential. Cluster analysis classified the 50 pepper accessions into six distinct groups. Additionally, genetic diversity analysis using molecular markers offers notable advantages due to its insensitivity to environmental factors and tissue specificity. Eleven highly polymorphic simple sequence repeat (SSR) markers were employed to assess the genetic diversity of the accessions. These markers allow for the detection of target genes at the seedling stage, enabling early selection of individuals with desirable traits and significantly expediting the breeding process. The findings of this study provide a solid theoretical foundation for the selection, utilization, and breeding of pepper germplasm resources.