Metabolic Pathways and Molecular Regulatory Mechanisms of Fruit Color Change During Greening Stage of Peppers (Capsicum annuum L.)

Our multi-omics investigation of pepper fruit coloration dynamics demonstrates that the coordinated regulation of flavonoid accumulation and chlorophyll retention underpins the distinct pigmentation patterns between dark green (XHB) and light green (QL2017) cultivars. Through the integrated analysis of three developmental stages (10-30 DPA), we identified 989 differentially accumulated metabolites (DAMs) and 810 differentially expressed genes (DEGs), with flavonoid biosynthesis, phenylpropanoid metabolism, and chlorophyll turnover pathways pinpointed as central regulatory hubs. Notably, key metabolites such as quercitrin, kaempferol-3-O-rhamnoside, and cinnamic acid were significantly enriched in dark green fruits (XHB), coinciding with enhanced antioxidant activity and delayed chlorophyll degradation. Transcriptomic data revealed the coordinated upregulation of chlorophyll biosynthesis genes (<i>COX15</i>, <i>POR</i>) and light-harvesting complex components (<i>Lhcb1</i>, <i>Lhcb2</i>), while <i>PAO</i>-a pivotal chlorophyll catabolism gene-also exhibited elevated expression. Co-expression network analysis highlighted <i>scopoletin GTase</i>, <i>F5H</i>, <i>CCR</i>, and <i>CAD</i> as hub genes regulating flavonoid biosynthesis. qRT-PCR validation confirmed high consistency with transcriptomic trends (<i>r</i> > 0.85, <i>p</i> < 0.01). Our findings propose a synergistic model wherein flavonoid accumulation and chlorophyll metabolic dynamics jointly orchestrate green fruit pigmentation, offering novel insights and molecular targets for the precision breeding of pepper fruit coloration.