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Natural variation of indels in the CTB3 promoter confers cold tolerance in japonica rice

Author

Listed:
  • Jin Li

    (China Agricultural University)

  • Haifeng Guo

    (China Agricultural University)

  • Qijin Lou

    (China Agricultural University)

  • Yawen Zeng

    (Yunnan Academy of Agricultural Sciences)

  • Zhenhua Guo

    (Rice Research Institute of Heilongjiang Academy of Agricultural Sciences)

  • Penghui Xu

    (China Agricultural University)

  • Yunsong Gu

    (China Agricultural University)

  • Shilei Gao

    (China Agricultural University)

  • Bingxia Xu

    (China Agricultural University)

  • Shichen Han

    (China Agricultural University)

  • Runbin Su

    (China Agricultural University)

  • Andong Zou

    (China Agricultural University)

  • Wei Ye

    (China Agricultural University)

  • Meng Zhang

    (China Agricultural University)

  • Yingxiu Li

    (China Agricultural University)

  • Xingming Sun

    (China Agricultural University)

  • Zhanying Zhang

    (China Agricultural University)

  • Hongliang Zhang

    (China Agricultural University)

  • Wendong Ma

    (Rice Research Institute of Heilongjiang Academy of Agricultural Sciences)

  • Chao Chen

    (Ltd)

  • Zichao Li

    (China Agricultural University)

  • Jinjie Li

    (China Agricultural University)

Abstract

Improvement of cold tolerance at the booting stage (CTB) in rice is a key strategy for cultivation in high-altitude and high-latitude regions. Here, we identify CTB3 gene, encoding a calmodulin-binding transcriptional activator that positively regulates cold tolerance at the booting stage in japonica rice. Two indels (57-bp and 284-bp) in the CTB3 promoter confer a differential transcriptional response to cold between the japonica and indica subspecies. OsTCP19 suppresses CTB3 expression by binding to these indels, negatively regulating cold tolerance. CTB3 activates the expression of TREHALOSE-6-PHOSPHATE PHOSPHATASE1 (OsTPP1), reducing trehalose 6-phosphate (Tre6P) levels, which increases sugar accumulation in panicles and improves cold tolerance. Additionally, favorable alleles of OsTCP19 and CTB3 are selected in japonica rice for cold adaptation. These findings highlight the important role of CTB3 in cold adaptation and its potential for improving cold tolerance in rice breeding.

Suggested Citation

  • Jin Li & Haifeng Guo & Qijin Lou & Yawen Zeng & Zhenhua Guo & Penghui Xu & Yunsong Gu & Shilei Gao & Bingxia Xu & Shichen Han & Runbin Su & Andong Zou & Wei Ye & Meng Zhang & Yingxiu Li & Xingming Sun, 2025. "Natural variation of indels in the CTB3 promoter confers cold tolerance in japonica rice," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56992-7
    DOI: 10.1038/s41467-025-56992-7
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    References listed on IDEAS

    as
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