Integrated transcriptomic and metabolomic analyses reveal transcriptional regulatory network for phenolic acid biosynthesis in potato tubers

The phenolic acid profile and concentration in potatoes signify their nutritional significance and functional value. In this study, a total of 398 metabolites, including 52 phenolic acids, were identified from three colored potato clones at three developmental stages using widely targeted metabolomics. Red and purple-fleshed potatoes exhibit higher levels of most phenolic acids compared to yellow-fleshed potatoes, particularly notable in their chlorogenic acid content. We concentrated on the distribution of differentially expressed transcription factors (TFs) among these clones, pinpointing the ERF (ethylene response factor), bHLH (basic helix-loop-helix), and MYB (myeloblastosis) as the predominant TFs via RNA-Seq analysis. Based on integrated transcriptomic and widely targeted metabolomic analysis, 23 pathway genes that might be involved in the biosynthesis of phenolic acid were identified. Furthermore, three central modules and several hub genes, encompassing 7 TFs, were identified. Notably, bHLH1 was identified as a key transcriptional regulator within this network, specifically activating the transcription of StCCoAOMT, , a key enzyme catalyzing the methylation of caffeoyl-CoA to feruloylCoA. This study may provide new insights into the molecular mechanisms of phenolic acid biosynthesis in potatoes and potentially advances the development of functional food products derived from these potatoes.