Plastic film mulching enhances flavonoid accumulation in the roots of Scutellaria baicalensis

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Background Scutellaria baicalensis Georgi is a medicinal herb of considerable importance, valued for its roots that are enriched with flavonoids underlying its pharmacological properties. A principal challenge in its commercial cultivation is the simultaneous enhancement of root biomass and the concentration of these active constituents. Although plastic film mulching is a well-established agronomic practice, its application to S. baicalensis and the corresponding molecular regulatory mechanisms remain insufficiently characterized. Methods This study systematically evaluated the effects of single- and double-layer plastic film mulching relative to an unmulched control on the agronomic traits of S. baicalensis . We employed an integrated analytical strategy, combining transcriptomic and broadly targeted metabolomic analyses of root and leaf tissues. Key regulatory networks and metabolic pathways were subsequently elucidated through weighted gene co-expression network analysis and pathway enrichment. Results Film mulching significantly promoted plant growth, with the double-layer application increasing root biomass by 417% compared to the control. Multi-omic analyses revealed a profound reprogramming of root transcription and metabolism in response to mulching. Transcriptomic shifts indicated the activation of central carbon metabolism, providing the energetic foundation for biomass accretion. Concurrently, metabolomic profiles confirmed a substantial increase in the accumulation of core flavonoids, including baicalin and baicalein. Integrative analysis implicated a regulatory network governed by WRKY and AP2/ERF transcription factors as central to this response. The upregulation of these transcription factors coincided with the synergistic activation of downstream enzyme genes in the flavonoid biosynthesis pathway, culminating in elevated flavonoid content. Conclusion Our findings demonstrate that plastic film mulching optimizes the rhizosphere to not only activate the primary metabolism requisite for rapid growth but also, acting as an environmental cue, to initiate a WRKY- and AP2/ERF-centric regulatory cascade that systematically enhances root-specific flavonoid biosynthesis. This work provides a molecular rationale for employing this agronomic strategy to achieve high-yield, high-quality cultivation of S. baicalensis .

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