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Background <p><i>C</i>-glycosyl flavones rarely accumulate at high levels in rice seeds, and the genetic basis underlying their biosynthesis and regulation remains poorly understood. The rice <i>yel</i>-<i>sdj</i> mutant, carrying a mutation in <i>DE-ETIOLATED 1</i> (<i>OsDET1</i>), shows elevated accumulation of <i>C</i>-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 <i>C</i>-glycosyl flavone biosynthesis in rice seeds.</p> Results <p>Transcriptomic profiling of developing seeds revealed that differentially expressed genes (DEGs) between wild-type and <i>yel</i>-<i>sdj</i> were significantly enriched in secondary metabolite and flavonoid biosynthetic pathways. Several genes associated with <i>C</i>-glycosyl flavone biosynthesis, including the rice <i>C</i>-<i>glycosyltransferase</i> (<i>OsCGT</i>), were upregulated in developing <i>yel</i>-<i>sdj</i> grains. To validate its function, we generated <i>OsCGT</i> knockout lines in the <i>yel</i>-<i>sdj</i> background. Loss of <i>OsCGT</i> markedly reduced the accumulation of <i>C</i>-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.</p> Conclusions <p>These findings demonstrate that <i>OsCGT</i> is essential for <i>C</i>-glycosyl flavone biosynthesis in <i>yel</i>-<i>sdj</i> seeds, particularly for isoorientin accumulation in the embryo, and indicate that embryo lethality is a fundamental consequence of the <i>OsDET1</i> mutation rather than <i>OsCGT</i>-dependent flavone accumulation. This study expands current understanding of flavonoid regulation in rice seeds and identifies <i>OsCGT</i> as a potential target for metabolic engineering to improve the nutraceutical and functional value of rice grains.</p>

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

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  • 发表日期：

    2026年7月18日

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  • Backki Kim,
  • Hee-Jin Choi,
  • Sangrae Shim,
  • Seong-Gyu Jang,
  • Dongryung Lee,
  • Endang M. Septiningsih,
  • Michael J. Thomson,
  • Seung-Hyun Kim,
  • Hee-Jong Koh,
  • Ill-Min Chung,
  • Soon-Wook Kwon

摘要

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.