Field Density Variation and Metabolite Profiling Reveal Transcriptome Mechanisms Driving Salt-Responsive Root Flavone Accumulation in Scutellaria baicalensis

Root flavones, especially baicalin, baicalein, wogonoside, and wogonin, contribute substantially to the medicinal quality of Scutellaria baicalensis Georgi. In the arid and semi-arid regions where this crop is grown, salinized soils constrain establishment but reshape specialized metabolism. We used field density trials, salt-stress experiments, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), and time-series RNA-seq, followed by weighted gene co-expression network analysis (WGCNA), to ask whether agronomic practices and salt-induced transcriptional changes alter root flavone content. Planting density showed a clear yield-quality trade-off: higher density increased belowground biomass per unit area but reduced individual root growth and flavone content, with 150 plants·m−2 providing a practical balance between population yield and root quality under the tested Xinjiang field conditions. In established seedlings, 0.5% NaCl caused no visible damage over 24 h and specifically raised baicalin and baicalein at 12 h, whereas wogonoside and wogonin (the wogonin-type flavones) remained nearly unchanged. Time-series RNA-seq identified thousands of differentially expressed genes between 2 and 24 h. WGCNA identified a turquoise module (one of the color-named co-expression modules) that was enriched for genes involved in carbohydrate metabolism and cytoskeletal/microtubule processes. Salt-responsive NAC, MYB and WRKY transcription factors co-expressed with core structural genes (PAL, 4CL, CHS, CHI); one candidate, SbNAC86, was up-regulated mainly at 24 h after the metabolite peak, consistent with a potential role in the later phase of the response rather than in triggering the initial accumulation peak. These findings outline the temporal dynamics of salt-induced branch-selective flavone accumulation and suggest candidate regulators for functional validation, with implications for quality-focused cultivation on saline marginal lands.