Transcriptome analysis reveals important regulatory genes and pathways for tuber color variation in Pinellia ternata (Thunb.) Breit.

During the growth of Pinellia ternata (Thunb.) Breit. (P. ternata), the violet-red skin was occasionally produced spontaneously under natural cultivation. However, the specific mechanism leading to the color change is still unclear. This study performed transcriptomes in violet-red and pale-yellow skin and their peeled tubers of P. ternata, and the total flavonoids and anthocyanin contents were also determined. The results showed that the majority of genes involved in anthocyanin production were considerably increased in the violet-red skin of P. ternata tuber compared to the pale-yellow skin. Especially, phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) showed a remarkable increase in gene expression levels. Notably, shikimate O-hydroxycinnamoyltransferase (HCT), naringenin 3-dioxygenase (F3H), flavanone 4-reductase (DFR), and anthocyanidin synthase (ANS) were explicitly expressed in violet-red skin of P. ternata tuber, while undetectable in pale-yellow skin. The upregulation of these genes may explain the accumulation of anthocyanins, which forms the violet-red skin of P. ternata tuber. The transcription factors, including C2H2, bZIP, ERF, GATA, bHLH, C3H, NAC, MYB-related, and MYB families, might trigger the skin color change in P. ternata. The entire anthocyanin content in the violet-red skin of P. ternata tuber was 71.10 μg/g, and pale-yellow skin was 7.74 μg/g. According to phenotypic and transcriptome results, the elevated expression levels of genes linked to the synthesis of anthocyanins considerably contributed to the violet-red skin alterations in P. ternata tuber. This study provides a new understanding of the formation of the violet-red skin, lays a theoretical foundation for the cultivation of unique varieties of P. ternata, and provides transcriptome data for further study of the differences between different colors of P. ternata.