Genome‐wide analysis, metabolomics, and transcriptomics reveal the molecular basis of <i>ZlRc</i> overexpression in promoting phenolic compound accumulation in rice seeds

Chinese wild rice (Zizania latifolia) is rich in phenolic compounds, particularly flavonoids. This study identified 203 basic helix-loop-helix (bHLHs) Z. latifolia and showed that ZlbHLH196 (Zla16G011250) corresponds to the ZlRc gene latifolia, with its protein product localizing nucleus. Notably, pericarps of ZlRc-overexpressing (OE) are brown, whereas those wild-type (WT) nonpigmented. The total phenolic, flavonoid, proanthocyanidin contents, antioxidant activity, as well enzyme inhibitory effects ZlRc-OE were significantly higher than WT rice. Overall, 221 differential metabolites between rice, among which 198 upregulated former. Additionally, a 227 differentially expressed genes 173 upregulated. Kyoto Encyclopedia Genes Genomes annotation enrichment analysis revealed enhanced isoflavonoid, flavone, flavonol, flavonoid biosynthesis pathways which, furthermore, markedly expression activities four key biosynthesis–related enzymes (phenylalanine ammonia-lyase, chalcone synthase, chalcone-flavanone isomerase, dihydroflavonol 4-reductase). These findings show ZlRc-overexpression promotes compound accumulation seeds can be used bioaugment content.