Association of Yellow-Orange Color of Ripe Pepper Fruits with Mutations in the Capsanthin-Capsorubin Synthase Gene CCS

In 12 varieties of pepper Capsicum spp., including red-fruited, orange-fruited, and yellow-fruited accessions, the content of carotenoids in ripe fruit was determined, including the characteristics of their composition in the peel and pulp. It has been shown that only red fruits contain the pigments capsanthin and capsorubin that determine this color. The color of the yellow-orange fruits was formed by a combination of α-/β-carotene, zeaxanthin, violaxanthin, and lutein. The structure of the capsanthin-capsorubin synthase gene CCS, responsible for synthesis capsanthin and capsorubin, was characterized in the studied varieties. Allelic variants of the gene were identified, including the functional allele A1, which is specific to red-fruited varieties and has a high level of transcripts in the fruit. The genome of yellow-orange accessions contained the A1Ψ (c599→a) allele, as well as the newly characterized allelic variants A1Ψ (g376→del), A2 and A3, the transcript levels of which in ripe fruit were low or zero. These alleles were characterized by a nonsense or a frameshift mutation (A1Ψ), an extended deletion of part of the promoter and the 5'-end of the CCS gene (A2), and putative critical changes in the promoter (A3). The presence of expression of key carotenogenesis genes (PSY1, LCYb, CrtZ), together with the carotenoid content data, indicated the absence of defects in the biosynthesis pathway of capsanthin and capsorubin precursors and a disruption in the CCS transcriptional regulation and/or the functionality of the encoded protein as the reason for the lack of capsanthin and capsorubin in yellow-orange fruits.