Genetic and environmental factors underlying variation in yield performance and bioactive compound content of hot pepper varieties (Capsicum annuum) cultivated in two contrasting Italian locations

Hot pepper (Capsicum spp.) is an economically considerable crop, particularly appreciated for its nutritional properties and antioxidants content. Levels of the latter depend on several factors including the cultivar and the environment. In the present study, diversity in morpho-agronomic traits and phytochemical compounds was investigated in 14 hot pepper accessions cultivated in two different pedoclimatic locations. The main source of variation was due to the genotype which showed significant differences for all traits at both locations. With regard to the bioactive compounds, the environment accounted for over 30% of variation for carotenoids, ascorbic acid and tocopherols and less than 0.5% for capsaicinoids. A strong genotype x environment interaction (p < 0.01) was observed in all traits with the exception of those related to fruit weight and shape. Genotyping by sequencing was used for molecular analysis revealing a total of 2120 single-nucleotide polymorphisms. Diversity on the basis of hierarchical clustering and structure analysis elucidated the relationships among accessions on the basis of their biological status and common ancestors, suggesting their contribution to the phenotypic performances observed. The comprehensive approach of this study provides useful information on the variability of phytochemicals mediated by the environment, revealing the challenge related to the genetic improvement of bioactive compounds. The integration of phenotypic and molecular data provides information to identify interesting hot pepper accessions to select for breeding programmes.