Natural variation of CTB5 confers cold adaptation in plateau japonica rice

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, Pingrong Yuan, Youliang Peng, Zichao Li () and Jinjie Li ()
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Haifeng Guo: 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

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-56174-5

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