Integrated metabolomic and transcriptomic analysis of metabolic diversity and biosynthesis of glucosinolates and flavonoids in various cultivars of radish microgreens

Microgreens, with their distinctive flavor and rapid growth, have garnered significant attention as a functional and nutritious food. In this study, we performed a thorough targeted metabolomic study using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS/MS) on four distinct cultivars of radish microgreens, namely Champion Radish (CR), White Radish (WR), Hailstone Radish (HR), and China Rose Radish (CRR), in order to better understand the metabolic foundation of the nutritional value of these microgreens. A total of 1411 metabolites were found and more than a third of the total number of metabolites were accounted for by flavonoids (FL), phenolic acids, lignans, coumarins and glucosinolates (GL). Significant variations were found in the differentially accumulated metabolites (DAM) and differentially expressed genes (DEG) in each pairwise comparison of cultivars, according to further comparative analysis. The comparison of CR with the other groups identified more than 400 DAM and about 10,000 DEG, the most abundant DAM being FL, and the results showed that CR was very different from WR, HR and CRR. A total of 33 GL were newly found in radish microgreens and classified into 8 categories according to their side chains. Weighted gene co-expression network analysis and biosynthetic pathway analysis revealed the distinctive relationship between gene expression levels and characteristic GL and FL. This work aimed to provide fresh insights into the differences in metabolite profiles among radish microgreens of various cultivars in addition to establishing a theoretical framework for improving the genetic quality of radish microgreens.