The Carrot Genome: A Framework to Study Health-Promoting Metabolite Accumulation

Carrot (Daucus carota subsp. carota L.) is among the top ten global vegetable crops and root crops both in terms of production and market value. Carrot is well recognized for its health properties which can be attributed to primary and secondary metabolites such as carotenoids, terpenoids, and anthocyanins. Metabolite accumulation represents an important trait in carrot production since it determines its nutritional value, color, taste and plays a critical role in human health. Despite their importance in carrot production little is known about the genetic mechanism controlling primary and secondary metabolite accumulation in carrot roots. Our group has led the development of the first chromosome scale assembly and characterization of the carrot genome. The assembly covers ~90% (422.3 Mb) of the estimated genome size (473 Mb) with an N50 of 12.7 Mb. Sixty superscaffolds covering 85.6% of the assembled genome were anchored to the nine pseudomolecules, containing over 95% of predicted genes. Genome characterization included a curated annotation of genes involved in the isoprenoid and flavonoid pathways and over 3,000 genes involved in regulatory function, including those controlling anthocyanin accumulation. A consensus linkage map integrating over 2,000 markers and 15 qualitative and quantitative traits, mainly related to metabolite accumulation, has been developed and anchored to the physical map. Integration of QTL mapping, transcriptome and genomic information are being used to identify candidate genes for metabolite accumulation.