Integrated Metabolome–Transcriptome Profiling Identifies JrMYB8 as a Repressor of Polyphenol Biosynthesis in Walnut (Juglans regia L.)

Walnut is valued for being rich in nutrients and polyphenols, which are key bioactive metabolites; however, a comprehensive and dynamic assessment of metabolites in the husk and pellicle is still lacking. In this study, multi-omics approaches combining untargeted metabolomics and transcriptome analysis were conducted to systematically characterize the differential metabolite profile and regulatory networks in walnut husk and pellicle. Metabolomic profiling revealed a clear divergence in polyphenol compositions between the husk and the pellicle; the husk was predominantly enriched in nine phenolic acid compounds, whereas the pellicle accumulated eleven flavonoid compounds. Through co-expression network analysis, a transcription factor, JrMYB8, was identified and shown to act as a specific inhibitor and regulator of polyphenol biosynthesis. Functional characterization demonstrated that JrMYB8 overexpression significantly reduced the accumulation of the total phenol content (TPC) and the total flavonoid content (TFC) by directly repressing the expression of JrC4H. These findings not only provide a molecular target for manipulating polyphenol content in walnut tissues but also offer a target for improving flavor in walnut breeding.