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Natural variation of CTB5 confers cold adaptation in plateau japonica rice

Author

Listed:
  • Haifeng Guo

    (China Agricultural University
    China Agricultural University)

  • Shilei Gao

    (China Agricultural University)

  • Huahui Li

    (Yunnan Academy of Agricultural Sciences)

  • Jiazhen Yang

    (Yunnan Academy of Agricultural Sciences)

  • Jin Li

    (China Agricultural University)

  • Yunsong Gu

    (China Agricultural University)

  • Qijin Lou

    (China Agricultural University)

  • Runbin Su

    (China Agricultural University)

  • Wei Ye

    (China Agricultural University)

  • Andong Zou

    (China Agricultural University)

  • Yulong Wang

    (China Agricultural University)

  • Xingming Sun

    (China Agricultural University)

  • Zhanying Zhang

    (China Agricultural University)

  • Hongliang Zhang

    (China Agricultural University)

  • Yawen Zeng

    (Yunnan Academy of Agricultural Sciences)

  • Pingrong Yuan

    (Yunnan Academy of Agricultural Sciences)

  • Youliang Peng

    (China Agricultural University)

  • Zichao Li

    (China Agricultural University)

  • Jinjie Li

    (China Agricultural University)

Abstract

During cold acclimation in high-latitude and high-altitude regions, japonica rice develops enhanced cold tolerance, but the underlying genetic basis remains unclear. Here, we identify CTB5, a homeodomain-leucine zipper (HD-Zip) transcription factor that confers cold tolerance at the booting stage in japonica rice. Four natural variations in the promoter and coding regions enhance cold response and transcriptional regulatory activity, enabling the favorable CTB5KM allele to improve cold tolerance. CTB5 interacts with OsHox12 and targets gibberellin (GA) metabolism genes to promote GAs accumulation in anthers and facilitate tapetum development under cold stress. Moreover, CTB5 directly regulates PYL9 and improves cold tolerance at the seedling stage by reducing reactive oxygen species (ROS) accumulation. The CTB5KM allele is selected during the cold acclimation of japonica rice to plateau habitats in Yunnan Province. Our findings provide insights into the mechanisms underlying cold adaptation in plateau japonica rice and offer potential targets for breeding cold-tolerant rice varieties.

Suggested Citation

  • Haifeng Guo & Shilei Gao & Huahui Li & Jiazhen Yang & Jin Li & Yunsong Gu & Qijin Lou & Runbin Su & Wei Ye & Andong Zou & Yulong Wang & Xingming Sun & Zhanying Zhang & Hongliang Zhang & Yawen Zeng & P, 2025. "Natural variation of CTB5 confers cold adaptation in plateau japonica rice," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56174-5
    DOI: 10.1038/s41467-025-56174-5
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