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

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