Cultivation regimes modulate flavonoid metabolism in rice: Integration of metabolomics and transcriptomics reveals NPK and density effects

Cultivation regimes significantly modulate flavonoid metabolism in rice panicles. Metabolomic analysis identified 257 flavonoids, with high-density planting (T0-T3) enhancing total diversity compared to conventional sparse planting (CK). The zero‑nitrogen high-density regime (T0) yielded the highest number (254). Differential analysis revealed 226 metabolites (DFMs), showing distinct correlations: nitrogen rate negatively correlated with 5 DFMs, phosphorus/potassium positively with 11 DFMs, and planting density correlated with 20 DFMs (11 positive, 9 negative). Transcriptomics identified 149 differentially expressed genes (DEGs) enriched in flavonoid pathways. Integration analysis established regulatory networks linking cultivation factors, key DFMs (e.g., kaempferol glycosides), and DEGs (notably 4CL, CHI). Crucially, optimized density (20.8 hills/m²) combined with balanced NPK (150-45-60 kg/hm²) and delayed nitrogen application (T3) synergistically enhanced functional flavonoids like kaempferol-3-O-galactoside, providing a strategy for high-quality rice production.