Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method

Radish ( Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070 , and four functional genes RsBRICK1 , RsBRI1-like2 , RsCOX1 , and RsCRK10 . In addition, some related genes such as RsCHS , RsCHI , RsANS , RsMT2-4 , RsUF3GT , glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.