Orange fruit color in Capsicum due to deletion of capsanthin-capsorubin synthesis gene

Fruit color of pungent pepper (Capsicum annuum L.) is a trait of economic importance in pepper breeding. To develop a system of molecular marker-assisted selection (MAS) for breeding pepper varieties with various fruit colors, we conducted molecular genetic analyses on six genes involved in the carotenoid biosynthesis pathway. Capsanthin-capsorubin synthase (CCS) gene showed a polymorphism in the PCR pattern in the segregation population derived from a cross between a pepper accession (cv. msGTY-1) with orange fruits and a pepper accession (cv. 277long) with red fruits. A deletion was found in the upstream region of the CCS gene in the plants with orange fruits. Southern hybridization analysis and sequencing analysis indicated that 211-bp of the downstream region of the gene was conserved in the plants with orange fruits, while no transcript of the CCS gene was detected by RT-PCR in the mature orange fruits. Carotenoid composition analysis using the Thin layer chromatography (TLC) method showed that one of the major pepper carotenoids, capsanthin, was present in the red fruits, but not in the orange fruits. The PCR polymorphism of the CCS gene and TLC pattern of carotenoid composition were completely cosegregated with the fruit color in the F-2 population, suggesting that the CCS gene determines the fruit color by changing the carotenoid composition.