Integrated transcriptomic and metabolomic analyses identify OsCGT as essential for C-glycosyl flavone biosynthesis in OsDET1-mutant rice seeds

BACKGROUND: C-glycosyl flavones rarely accumulate at high levels in rice seeds, and the genetic basis underlying their biosynthesis and regulation remains poorly understood. The rice yel-sdj mutant, carrying a mutation in DE-ETIOLATED 1 (OsDET1), shows elevated accumulation of C-glycosyl flavones in the embryo and pericarp, providing a useful system for dissecting the molecular mechanisms controlling these metabolites. Here, we performed comparative transcriptomic and metabolomic analyses, together with genome-editing-based functional validation, to identify key genes involved in C-glycosyl flavone biosynthesis in rice seeds. RESULTS: Transcriptomic profiling of developing seeds revealed that differentially expressed genes (DEGs) between wild-type and yel-sdj were significantly enriched in secondary metabolite and flavonoid biosynthetic pathways. Several genes associated with C-glycosyl flavone biosynthesis, including the rice C-glycosyltransferase (OsCGT), were upregulated in developing yel-sdj grains. To validate its function, we generated OsCGT knockout lines in the yel-sdj background. Loss of OsCGT markedly reduced the accumulation of C-glycosyl flavones, particularly isoorientin, in the embryo and restored embryo coloration to a wild-type-like phenotype. In contrast, despite the significant reduction in C-glycosyl flavone accumulation, pericarp pigmentation was not obviously altered, and embryo lethality was not rescued. CONCLUSIONS: These findings demonstrate that OsCGT is essential for C-glycosyl flavone biosynthesis in yel-sdj seeds, particularly for isoorientin accumulation in the embryo, and indicate that embryo lethality is a fundamental consequence of the OsDET1 mutation rather than OsCGT-dependent flavone accumulation. This study expands current understanding of flavonoid regulation in rice seeds and identifies OsCGT as a potential target for metabolic engineering to improve the nutraceutical and functional value of rice grains.