Transcriptome analyses reveal key genes involved in skin color changes of 'Xinlimei' radish taproot

The color of radish (Raphanus sativus) taproot skin is an important visual quality. 'Xinlimei' radish is a red-fleshed cultivar with skin that changes color from red to white and finally to green at the mature stage, and appearance quality is strongly affected if the red color does not fade completely on a single taproot or simultaneously among different taproots. In the present study, anthocyanin and chlorophyll contents and the transcriptome of radish taproot skin at three distinct coloration stages were analyzed to explore the mechanism of color changes. The results showed that decreased anthocyanin and increased chlorophyll contents correlated with the color-fading process. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of differentially expressed genes indicated that anthocyanin and chlorophyll metabolism pathways play important roles in color changes. In red color-fading process, the expression levels of anthocyanin biosynthetic genes (except PAL and C4H), a transport gene (RsTT19), and two anthocyanin biosynthesis transcription factors (TFs), RsMYB1 and RsTT8, were significantly downregulated, whereas peroxidase-encoding genes were significantly upregulated. In the skin-greening process, expression of most chlorophyll biosynthetic genes and two TFs (RsGLK1 and RsGLK2) that likely positively regulate chlorophyll biosynthesis was significantly upregulated. Thus, changes in the expression of these genes may be responsible for the color changes that occur in 'Xinlimei' taproot skin. This is the first report on the roles of chlorophyll metabolism genes and their dynamic relationship with anthocyanin metabolism genes in radish. The findings provide valuable information and theoretical guidelines for improving the appearance quality of 'Xinlimei' radish taproots.