Genome-wide identification and expression analysis of the carotenoid metabolic pathway genes in pepper (Capsicum annuumL.)

Carotenoids belong to a major family of isoprenoids which play vital roles in plant growth and development. Pepper (Capsicum annuumL.) is not only a vegetable and condiment grown worldwide, but also can be used as a model organism in fruit color research. In this study, 61 genes known to be involved in mevalonate (MVA), plastidial 2-C-methyl-d-erythritol-4-phosphate (MEP) and carotenoid metabolism (biosynthesis and catabolism) pathways were identified and characterized based on the genome of pepper plants. In the present study, it was found that 56 of the 61 carotenoid metabolism genes in pepper were unevenly distributed throughout 12 chromosomes.CaGGPPS2,CaGGPPS4aandCaGGPPS4bwere generally clustered into one region. This study identifiedCaHMGR1/CaHMGR3andCaHMGR1/CaHMGR2as segregation duplication events. In addition, the pepper carotenoid metabolism genes had high variations in gene structure. The key carotenoid metabolism genes showed different expression patterns during the pepper fruit development and under environmental stress conditions. The results obtained in this research investigation will contribute insight to the evolution and function of carotenoid metabolic pathways in pepper fruit.