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

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, Zhanying Zhang, Hongliang Zhang, Wendong Ma, Chao Chen, Zichao Li and Jinjie Li ()
Additional contact information
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

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-56992-7

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