Orange color is associated with CYC-B expression in tomato fleshy fruit

Carotenes are plant secondary metabolites that are important for human health. Additionally, carotenes influence fruit color, which is a major trait for breeding. We compared the expression and sequences of genes related to color phenotypes in tomato inbred lines that produce different colors of fleshy fruit. Up-regulation of CYC-B expression and higher amount of β-carotene content in fruit ripening stage and nucleotide variations in the 5′ region of the gene were detected in orange fruited inbred lines compared to the other lines. Our results indicated that there is a close relationship between the expression pattern of the CYC-B gene and the orange color of fleshy fruit. We identified 4 SNPs in the promoter region of CYC-B genes associated with the orange fruit color. Moreover, the segregation ratio and color phenotypes in an F2 generation further indicated that one of the detected SNPs were associated with the orange color in the tested inbred lines. Our study provides valuable information to breeders for marker-assisted selection to produce desirable tomato varieties with health benefits by varying carotenoid levels.