Transcriptomic dynamics changes in development 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. However, transcriptome analysis of anthocyanin biosynthesis and expression of anthocyanin biosynthesis related genes in ‘Hongxin’ radish have not been fully investigated. Here, based on results from HPLC analysis, young fleshy roots obtained from the dynamics development stage of fleshy roots in carmine radish ‘Hongxin 1’ was used for RNA-Seq, including fleshy 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 roots in carmine radish were identified. After that, DGE (differential gene expression) profile analysis was used to identify the pupative transcripts, compared with fleshy roots from seedling stage (SS). In addition, co-modulated DEGs (Common DEGs in the dynamic growing stages of fleshyroot in carmine radish) were also identified, from which most DGEs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB and Rs RZFP . 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 roots. 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 roots after initial expansion of fleshy roots. Moreover, these results indicated that five significantly enrichment pathways of DEG were identified for the dynamics growing stages of fleshy 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 fleshyroot in carmine radish.