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

Abstract

BackgroundAnthocyanins 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.ResultsRNA 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).ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5135-6) contains supplementary material, which is available to authorized users.

Changing Carrot Color: Insertions in DcMYB7 Alter the Regulation of Anthocyanin Biosynthesis and Modification

“…In addition, purple carrot root pigmentation extensively varies across different carrot genotypes, ranging from the purple peridermal carrot type (purple periderm but nonpurple phloem and xylem) to the solid purple carrot type (purple periderm, phloem, and xylem). The genetic control of anthocyanin pigmentation in purple carrots has been investigated (Simon, 1996;Yildiz et al, 2013;Cavagnaro et al, 2014;Xu et al, 2014Xu et al, , 2016Xu et al, , 2017Kodama et al, 2018;Iorizzo et al, 2019). Two genes that condition the anthocyanin pigmentation of carrot roots from different genetic backgrounds, P 1 and P 3 , have been identified and genetically mapped within 28.2-and 12-centimorgan regions, respectively, on chromosome 3, supporting the theory of two independent mutation and human selection events during the domestication of purple carrots (Cavagnaro et al, 2014).…”

Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry

“…The regulation of LBG activity by the MBW complex is well conserved among land plants, and several studies report the functional characterization of MBW members through transgenic expression in orthologous system [ 61 , 62 , 72 , 88 , 89 , 90 , 91 , 92 , 93 , 94 ]. Among 891 MYB-, bHLH- and WD40-coding genes mapped in the carrot genome by Iorizzo et al (2019), 73 genes are potentially related to the anthocyanin metabolism through one of the following three criteria: overlapping with an anthocyanin-related QTL, differentially expressed between purple and non-purple tissues, or orthologous to a known anthocyanin-related gene from another species ( Supplementary Table S4 ) [ 34 , 52 , 67 , 71 , 72 , 95 ]. Only 12 of them, including 11 anthocyanin-related MYBs ( A-MYBs ) and 1 anthocyanin-related bHLH ( A-bHLH ), DcbHLH3 , possessed all three criteria, and therefore represent primary candidates for further investigating the regulation of purple pigmentation in carrot ( Table 3 ).…”

De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

“…At present, transcriptome sequencing technology has been used to study vegetables color formation [28], ower color mechanisms [10,29], fruit development [30,31]. Some scholars have analyzed the color mechanism of the related species in Acer [32].…”