Transcriptomic dynamics changes related to anthocyanin accumulation in the fleshy roots of carmine radish (Raphanus sativus L.) characterized using RNA-Seq

Abstract

Carmine radish is famous for containing a natural red pigment (red radish pigment). However, the expression of anthocyanin biosynthesis-related genes during the dynamic development stages of the fleshy roots in carmine radish has not been fully investigated. Here, based on HPLC quantification of anthocyanin levels from our previous study, young fleshy roots of the carmine radish “Hongxin 1” obtained at the dynamic development stages of fleshy roots (seedling stage (SS), initial expansion (IE), full expansion (FE), bolting stage (BS), initial flowering stage (IFS), full bloom stage (FBS) and podding stage (PS)) were used for RNA-Seq. Approximately 126 comodulated DEGs related to anthocyanin biosynthesis (common DEGs in the dynamic growth stages of fleshy roots in carmine radish) were identified, from which most DEGs appeared to be 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, RsGSTF12, RsUFGT78D2 and RsUDGT-75C1, were found as candidate contributors to the regulatory mechanism of anthocyanin synthesis in the fleshy roots of carmine radish. In addition, 11 putative DEGs related to anthocyanin synthesis were evaluated by qRT-PCR via the (2-ΔΔCT) method; the Pearson correlation analysis indicated excellent concordance between the RNA-Seq and qRT-PCR results. Furthermore, GO enrichment analysis showed that “anthocyanin-containing compound biosynthetic process” and “anthocyanin-containing compound metabolic process” were commonly overrepresented in the dynamic growth stages of fleshy roots after the initial expansion stage. Moreover, five significantly enriched pathways were identified among the DEGs in the dynamic growth stages of fleshy roots in carmine radish, namely, flavonoid biosynthesis, flavone and flavonol biosynthesis, diterpenoid biosynthesis, anthocyanin biosynthesis, and benzoxazinoid biosynthesis. In conclusion, these results will expand our understanding of the complex molecular mechanisms of anthocyanin biosynthesis in the fleshy roots of carmine radish and the putative candidate genes involved in this process.

Integrated physiological, transcriptomics and metabolomics analysis revealed the molecular mechanism of Bupleurum chinense seedlings to drought stress

“…To validate the transcriptome data, real-time fluorescence quantitative PCR (qRT-PCR) were performed on seven DEGs with a| log 2 ratio| between 2 and 10, and high expression levels in the leaves and roots of B . chinense under drought stress [ 36 ]. Primer Premier 5.0 was used to design specific primers.…”

Radish (Raphanus Sativus): Potential antioxidant role of bioactive compounds extracted from radish leaves - A review

“…The highest 38.8% of reported data were flavonoids. Other reported compounds were non-flavonoid polyphenols 8.4%, Terpenes and derivatives 8.2%, fat and fatty related compounds 6.4% and glucosinolates and breakdown products 5.6% 4,25,26,27 . A specific aliphatic glucosinolate (GSL), Glucoraphasatin (GRH) is that is only abundant in radish.…”

Comparative Transcriptome Analysis of the Roots and Leaves of Bupleurum Chinense DC. Seedlings Under Drought Stress

“…In order to verify the transcriptome data, seven DEGs with 2 ≤ | log 2 ratio| ≤ 10 and high expression levels were selected from the DEGs of leaves and roots of B. chinense under drought stress for qPCR veri cation [45]. The actin gene of B. chinense was used as internal control.…”