Orange Is the New Yellow: Cracking the Genetic Code Controlling Carotenoid Accumulation in Carrot (Daucus carota L.)

Orange carrots (Daucus carota L.) are one of the highest naturally occurring vegetable sources of provitamin A. The orange pigment in carrot, which is primarily beta-carotene, can be represented as two connected retinal groups that are enzymatically cleaved in the body to contribute to vitamin A levels.  Vitamin A is important for good vision, a healthy immune system, and normal cell growth.  To ascertain how genes in the carotenoid biosynthetic pathway contribute to beta-carotene accumulation, several studies have used the candidate gene approach. However, these studies have only found weak associations. We are interested in taking a whole genome approach to identify candidate genes involved in beta-carotene accumulation. To develop genome-wide markers, we used the Genotyping-by-Sequencing technique on a F4 mapping population which was segregating for beta-carotene accumulation. Phenotypic data was collected using High Performance Liquid Chromatography. 6,363 uniquely mapped SNPs were identified and used in a General Linear Model analysis in the TASSEL application.  A localized region (~1Mb) on Chromosome 7 was found to be significantly associated with beta-carotene accumulation. To further narrow the list of candidate genes within this region we conducted an RNA-Sequencing experiment using orange and yellow pigmented roots. Within the genomic area of interest, 14 genes were found to be differentially expressed.  Fine-mapping, genome-annotation, and functional assays are currently underway to further characterize the genetic control of beta-carotene accumulation in carrot.