Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.)

  • Florencia Bannoud
  • Shelby Ellison
  • Marcos Paolinelli
  • Thomas Horejsi
  • Douglas Senalik
  • Martín Fanzone
  • Massimo Iorizzo
  • Philipp W. SimonEmail author
  • Pablo F. CavagnaroEmail author
Original Article


Key message

Inheritance, QTL mapping, phylogenetic, and transcriptome (RNA-Seq) analyses provide insight into the genetic control underlying carrot root and leaf tissue-specific anthocyanin pigmentation and identify candidate genes for root phloem pigmentation.


Purple carrots can accumulate large quantities of anthocyanins in their root tissues, as well as in other plant parts. This work investigated the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root phloem and xylem, and in leaf petioles. Inheritance of anthocyanin pigmentation in these three tissues was first studied in segregating F2 and F4 populations, followed by QTL mapping of phloem and xylem anthocyanin pigments (independently) onto two genotyping by sequencing-based linkage maps, to reveal two regions in chromosome 3, namely P1 and P3, controlling pigmentation in these three tissues. Both P1 and P3 condition pigmentation in the phloem, with P3 also conditioning pigmentation in the xylem and petioles. By means of linkage mapping, phylogenetic analysis, and comparative transcriptome (RNA-Seq) analysis among carrot roots with differing purple pigmentation phenotypes, we identified candidate genes conditioning pigmentation in the phloem, the main tissue influencing total anthocyanin levels in the root. Among them, a MYB transcription factor, DcMYB7, and two cytochrome CYP450 genes with putative flavone synthase activity were identified as candidates regulating both the presence/absence of pigmentation and the concentration of anthocyanins in the root phloem. Concomitant expression patterns of DcMYB7 and eight anthocyanin structural genes were found, suggesting that DcMYB7 regulates transcription levels in the latter. Another MYB, DcMYB6, was upregulated in specific purple-rooted samples, suggesting a genotype-specific regulatory activity for this gene. These data contribute to the understanding of anthocyanin regulation in the carrot root at a tissue-specific level and maybe instrumental for improving carrot nutritional value.



The authors acknowledge the BEC.AR Scholarship Program of the Argentine Ministry of Education. FB and MP were supported by the Argentine National Council of Scientific and Technical Research (CONICET) PhD and postdoctoral fellowships, respectively. This work was partly funded by the ‘Agencia Nacional de Promoción Científica y Tecnológica’ through grant ‘Préstamo BID PICT-2015-1625.’ SE was supported by the National Institute of Food and Agriculture, the USA Department of Agriculture (NIFA-USDA), under Award Number 2016-51181-25400. MI was supported by the USA Department of Agriculture National Institute of Food and Agriculture, Hatch Project 1008691.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

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Supplementary material 1 (DOCX 23861 kb)
122_2019_3366_MOESM2_ESM.xlsx (1.1 mb)
Supplementary material 2 (XLSX 1172 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos AiresArgentina
  2. 2.USDA-Agricultural Research Service, Vegetable Crops Research UnitUniversity of Wisconsin-MadisonMadisonUSA
  3. 3.Instituto Nacional de Tecnología Agropecuaria INTA EEA MendozaMendozaArgentina
  4. 4.Plants for Human Health InstituteNorth Carolina State UniversityKannapolisUSA
  5. 5.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA
  6. 6.Department of HorticultureUniversity of Wisconsin-MadisonMadisonUSA
  7. 7.Instituto de Horticultura, Facultad de Ciencias AgrariasUniversidad Nacional de CuyoMendozaArgentina
  8. 8.Instituto Nacional de Tecnología Agropecuaria (INTA) - E.E.A. La ConsultaSan CarlosArgentina

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