Integrated metabolomics and transcriptomics analysis provides insights into biosynthesis and accumulation of flavonoids and glucosinolates in different radish varieties

Radish is an important vegetable worldwide, with wide medicinal functions and health benefits. The quality of radish, strongly affected by phytochemicals like flavonoids and glucosinolates, are quite different depending on the radish varieties. However, the comprehensive accumulation profiles of secondary metabolites and their molecular regulatory mechanisms in different radish cultivars remain unclear thus far. Herein, we comprehensively analyzed the secondary metabolite and gene expression profiles of the flesh and skin of four popular radish varieties with different flesh and/or skin colors, using UPLC-MS/MS-based metabolomics and transcriptomics approach combined with RT-qPCR. The results showed that altogether 352 secondary metabolites were identified in radish, of which flavonoids and phenolic acids accounted for 60.51% of the total. The flesh and skin of each variety exhibited distinct metabolic profiles, making them unique in coloration, flavor, taste, and nutritional quality. The differential metabolites were mostly enriched in flavonoid biosynthesis, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and glucosinolate biosynthesis pathway. Further, 19 key genes regulating the differential accumulation of flavonoids among different radish varieties were identified, such as <i>RsCHS</i>, <i>RsCCOAMT</i>, <i>RsF3H</i>, <i>RsFLS</i>, <i>RsCYP75B1</i>, <i>RsDFR</i>, and <i>RsANS</i> that were significantly upregulated in red-colored radish tissue. Also, 10 key genes affecting the differential accumulation of glucosinolates among different varieties were identified, such as <i>RsCYP83B1</i>, <i>RsSUR1</i>, and <i>RsST5a</i> that were significantly increased in the skin of green radish. Moreover, systematical biosynthetic pathways of flavonoids and glucosinolates and co-expression networks between genes and metabolites were constructed based on integrative analysis between metabolomics and transcriptomics. Our findings provide a novel insight into the mechanisms of radish quality formation, thereby providing a molecular basis for breeding and cultivation of radish with excellent nutritional quality.