Genetic diversity of Capsicum chinense accessions based on fruit morphological characterization and AFLP markers

Capsicum chinense is one of the most cultivated and consumed chili pepper species in Brazil, and Amazon Basin is considered domestication center for the species. C. chinense is known for the impressive morphological fruit variability, which can be characterized by different shapes, colors, sizes, and pungency levels. In this study we report the characterization of 71 C. chinense accessions from different Brazilian geographic regions using fruit morphological descriptors and AFLP molecular markers. Fourteen descriptors, eight qualitative and six quantitative, were used to fruit characterization. For AFLP analysis, seven combinations of EcoRI and MseI primers were tested, and the following combinations were selected: E-ACA/M-CAC, E-ACC/M-CAA, and E-ACG/M-CAA. Morphological data were analyzed using WARD-MLM procedure, while Ward clustering and Bayesian procedure were used for molecular analysis. Variability was found in C. chinense in Brazil in terms of fruit phenotype, resulting in three clusters. Fruit shape and fruit weight characteristics were essential for distributing the accessions. Molecular data produced 302 polymorphic bands, forming two groups. It was not possible to group the accessions solely based on their origin using the fruit morphological data and molecular data. There was also no association between the morphological descriptors and AFLP markers. The lack of correlation suggests that both characterization steps are important for understanding and differentiating the C. chinense accessions. The combination of morphological and molecular analyses is suggested for the complete and detailed characterization of germplasm databases.