Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root

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

We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.EEA La ConsultaFil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados UnidosFil: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados UnidosFil: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Peng, Zeng. Beijing Genomics Institute–Shenzhen; ChinaFil: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados UnidosFil: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; ChinaFil: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados UnidosFil: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; ItaliaFil: Sanseverino, Walter. Sequentia Biotech; EspañaFil: Cavagnaro, Pablo Federico. . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; TurquíaFil: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; PoloniaFil: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados UnidosFil: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; ChinaFil: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; ChinaFil: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados UnidosFil: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados UnidosFil: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unido