Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq

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  • Miyako Kodama, Genome Research and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. miyako.kodama@bio.ku.dk., Natural History Museum of Denmark, University of Copenhagen
  • ,
  • Henrik Brinch-Pedersen
  • Shrikant Sharma
  • Inger Bæksted Holme
  • Bjarne Joernsgaard, Chr. Hansen Natural Colors A/S, Taastrup, Denmark.
  • ,
  • Tsaneta Dzhanfezova, Chr. Hansen Natural Colors A/S, Taastrup, Denmark.
  • ,
  • Daniel Buchvaldt Amby, Natural History Museum of Denmark, University of Copenhagen, Department of Plant Protection Biology, Swedish University of Agricultural Sciences
  • ,
  • Filipe Garrett Vieira, Natural History Museum of Denmark, University of Copenhagen
  • ,
  • Shanlin Liu, Natural History Museum of Denmark, University of Copenhagen, BGI-Shenzhen, Shenzhen 518083, China
  • ,
  • M Thomas P Gilbert, Natural History Museum of Denmark, University of Copenhagen, NTNU University Museum, Erling Skakkes gate 47A, 7012, Trondheim, Norway.

BACKGROUND: Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible for their biosynthesis are not well characterized. The current study aimed to analyze global transcription profiles based on RNA sequencing (RNA-Seq), and mine MYB, bHLH and WD40 genes that may function as positive or negative regulators in the carrot anthocyanin biosynthesis pathways.

RESULTS: RNA was isolated from differently colored calli, as well as tissue samples from taproots of various black carrot cultivars across the course of development, and gene expression levels of colored and non-colored tissue and callus samples were compared. The expression of 32 MYB, bHLH and WD40 genes were significantly correlated with anthocyanin content in black carrot taproot. Of those, 11 genes were consistently up- or downregulated in a purple color-specific manner across various calli and cultivar comparisons. The expression of 10 out of these 11 genes was validated using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR).

CONCLUSIONS: The results of this study provide insights into regulatory genes that may be responsible for carrot anthocyanin biosynthesis, and suggest that future focus on them may help improve our overall understanding of the anthocyanin synthesis pathway.

Original languageEnglish
Article number811
JournalBMC Genomics
Volume19
Pages (from-to)1-13
Number of pages13
ISSN1471-2164
DOIs
Publication statusPublished - 8 Nov 2018

    Research areas

  • Daucus carota L., Anthocyanin, RNA-Seq, Differential expression analyses, Transcription Factors

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