Carrot Carotenoid Genetics and Genomics

Abstract

Carotenoids are essential for photosynthesis, and they are the ultimate source of all dietary vitamin A. They account for the striking diversity of orange, yellow, and red carrot storage root color, and this likely contributes to the fact that carotenoids are the most extensively studied class of compounds in carrot, where their biosynthesis and accumulation have been evaluated across diverse genetic backgrounds and environments. Many genes in the 2-C-methyl-D-erythritol-4-phosphate pathway (MEP) and carotenoid biosynthetic pathways have been identified and characterized in carrot, and genes in those pathways are expressed in carrot roots of all colors, including white carrots which contain at most trace amounts of carotenoids. The active functioning of genes in the carotenoid pathway in carrot roots of all colors should be expected since pathway products serve as precursors for hormones important in plant development. 1-Deoxy-d-xylulose-5-phosphate synthase (DXS) in the MEP pathway and the phytoene synthase and lycopene β-cyclase (PSY, LCYB) genes in the carotenoid pathway provide some level of overall regulation or modulation of these respective pathways, and these genes are incrementally upregulated in carrots with higher carotenoid content but variation in their expression does not account for the diverse content and composition of carotenoids in different colors of carrots. In contrast, genetic polymorphism in the Y and Y2 genes accounts for much for the variation in carotenoids accumulated in white, yellow, and orange carrots, and with the sequencing of the carrot genome, the genetic basis for these genes is becoming revealed. A candidate for the Y gene, DCAR_032551, is not a member of either the MEP or carotenoid biosynthesis pathway but rather a regulator of photosystem development and carotenoid storage. A clear candidate for the Y2 gene has not been identified, but no carotenoid biosynthetic gene was found in the genomic region defined by fine mapping of Y2. The Or gene, which regulates chromoplast development in other crops, was also recently associated with the presence of carotenoids in carrot. The discovery of genes outside the carotenoid biosynthetic pathway that contributes to carotenoid colors of carrots is but one exciting consequence of sequencing the carrot genome.