Transcriptomic dynamics changes related to anthocyanin biosythesis of carmine radish (Raphanus sativus L.) fleshy roots using RNA-seq method

Radish (Raphanus sativus L.), belonging to biennial root vegetable crop of Brassicaceae family, is an economically important vegetable crop with an edible taproot. Recently, most of differential expressed genes associating with anthocyanin biosynthesis have been identified in most of important fruit crops using RNAseq technology. However, transcriptome analysis of anthocyanin biosynthesis and expression of anthocyanin biosynthesis related genes in ‘Hongxin’ radish (That is famous for containing natural red pigment (red radish pigment), as produced in Chongqing Fuling named for Fuling three specialties) have not been fully investigated. Here, based on results from HPLC analysis, young fleshy roots obtained from the dynamics development stage of fleshy root in carmine radish ‘Hongxin 1’ was used for RNA-Seq, including flesh roots from seedling stage (SS), initial expansion (IE), full-expansion (FE), bolting stage (BS), initial flowering stage (IFS); full-bloom stage (FBS) and podding stage (PS). Subsequently, the putative candidate genes involved in the dynamics development stage of fleshy root in carmine radish were identified. After that, DGE (differential gene expression) profile analysis was used to identify the pupative transcripts, compared with flesh roots from seedling stage (SS). In addition, co-modulated DEGs (Common DEGs in the dynamic growing stages of fleshy root in carmine radish) were also identified, from which most DGEs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB and RsRZFP. In addition, some related proteins e.g. RsCHS, RsDFR, RsANS, RsF’3H, RsF3GGT1, Rs3AT1, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like were significantly contributed to the regulatory mechanism during anthocyanin synthesis in the development stage of fleshy root. Furthermore, GO terms comprised of “anthocyanin-containing compound biosynthetic process” and “anthocyanin-containing compound metabolic process” were commonly overrepresented in the other dynamics growing stages of fleshy root after initial expansion of fleshy root. Moreover, these results indicated that five significantly enrichment pathways of DEG were identified for the dynamics growing stages of flesh roots in carmine radish, including Flavonoid biosynthesis, Flavone and flavonol biosynthesis, Diterpenoid biosynthesis, Anthocyanin biosynthesis, as well as Benzoxazinoid biosynthesis. These results will expand our understanding of complex molecular mechanism of the putative candidate genes involved in the dynamics development stage of fleshy root in carmine radish.