Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples. 120-day-old carrot taproots of three cultivars (‘H13.360IND’, ‘Purple 68’, and ‘Purple Haze’) were used. For H31.360IND, the whole slice was used; for ‘Purple 68’ and ‘Purple Haze’ the carrot discs were dissected into the xylem and phloem tissue samples. Following this, RNA-Seq libraries were constructed and labeled as follows: CT (whole slice of H13.360IND), E (xylem of ‘Purple 68’), F (phloem of ‘Purple 68’), G (xylem of ‘Purple Haze’) and H (phloem of ‘Purple Haze’). Two biological replicates were used for each sample using Illumina® (NEB, USA).