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Title: A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Author
item IORIZZO, MASSIMO - University Of Wisconsin
item ELLISON, SHELBY - University Of Wisconsin
item Senalik, Douglas
item ZENG, PENG - Bgi Shenzhen
item SATAPOOMIN, PIMCHANOK - University Of Wisconsin
item BOWMAN, MEGAN - Michigan State University
item IOVENE, MARINA - National Research Council - Italy
item SANSEVERINO, WALTER - University Of Barcelona
item CAVAGNARO, PABLO - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET)
item YILDIZ, MEHTAP - Yuzuncu Yil Centennial University
item MACKO-PODGORNI, ALICJA - University Of Agriculture - Poland
item Spooner, David
item Simon, Philipp

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2016
Publication Date: 5/9/2016
Publication URL: http://handle.nal.usda.gov/10113/62647
Citation: Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., Yildiz, M., Spooner, D.M., Simon, P.W., et al. 2016. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics. 48(6):657-666. doi: 10.1038/ng.3565.

Interpretive Summary: Carrots are among the top 10 vegetable crops in the U.S. and worldwide, and an important source of vitamin A in the U.S. diet. Development of genetic tools for carrot breeding has progressed in recent decades, but relatively little information on the carrot genome is available. In this project, we sequenced the carrot genome and based on this information, we evaluated the evolution of carrots relative to related crops, we identified genes involved in basic cellular function, disease and stress resistance, pigment and flavor compound biosynthesis and accumulation, and we developed a molecular model for the major gene accounting for yellow and orange pigments in the carrot root. This research is of interest for genomics and evolutionary biology researchers, nutritionists, plant breeders, and the seed industry.

Technical Abstract: We report a chromosome-scale assembly and analysis of the Daucus carota genome, an important source of provitamin A in the human diet and the first sequenced genome among members of the Euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Euasterid I clade, clarifying the evolutionary scenario before and after the radiation of the two main Asterid clades. Large- and small-scale lineage-specific duplications contributed to the expansion of gene families including those with roles in flowering time, defense response, flavor, and pigment accumulation. We demonstrated that the primary genetic locus underlying carotenoid accumulation in the carrot root, that is the foundation of the orange color of modern carrots, is not directly controlled at the biosynthetic level. A candidate gene was identified, and transcriptome data suggested that high carotenoid accumulation involves overexpression of several light-induced genes operating in photosystem development and function. These results provide a resource for crop improvement, for comparative genome analysis in the Asterid lineage, and for the discovery of novel genetic mechanisms regulating carotene biosynthesis and accumulation in plants.