Integrated Metabolome–Transcriptome Profiling Identifies JrMYB8 as a Repressor of Polyphenol Biosynthesis in Walnut (<i>Juglans regia</i> 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 <i>JrMYB8</i> overexpression significantly reduced the accumulation of the total phenol content (TPC) and the total flavonoid content (TFC) by directly repressing the expression of <i>JrC4H</i>. 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.