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Journal of Integrative Agriculture
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A Caseinolytic proteases ATPase family gene OsClpI3 contributes to thermotolerance in rice

Fengfeng Fan2*#, Zihan Yang2*, Huanran Yuan3*, Ayaz Ahmad2, Kai Lv1, Fei Xu1, Manman Liu2, Yu Guo2, Fengfeng Si2, Nengwu Li2, Shaoqing Li2#, Mingxing Cheng1, 2#

1 Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan 430072, China.

2 State Key Laboratory of Hybrid Rice/Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture and Rural Affairs/Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education/College of Life Science, Wuhan University, Wuhan 430072, China

3 Hubei Shizhen Laboratory, Wuhan 430072, China

 Highlights 

OsClpI3 is a newly discovered gene that contributes to heat tolerance in rice.

OsClpI3 contributes to maintaining photosynthetic electron transport and net photosynthetic rate in rice under heat stress.

Natural variation in OsClpI3 gene sequences controls heat tolerance in rice.

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摘要  

全球气温的持续升高以及极端高温事件的频发,对水稻生产构成了严峻挑战。挖掘耐热基因并培育耐热水稻品种,是应对这一问题的有效策略。本研究通过对酪蛋白水解酶(ClpATP酶基因家族的分析,鉴定出一个新型耐热基因OsClpI3OsClpI3主要在叶片中表达,编码一个叶绿体定位蛋白,并在水稻的苗期和抽穗期均正向调控耐热性。OsClpI3具有ATP酶活性,而在敲除突变体中该活性显著降低。联合转录组和代谢组分析表明,OsClpI3通过维持高温条件下的光合电子传递效率及整体光合性能贡献于水稻耐热性。此外,OsClpI3的自然变异影响水稻耐热性,并且单倍型分析揭示了一种优良耐热单倍型Type4。这些结果不仅为阐明水稻耐热性的分子机制提供了新的见解,也为培育耐热水稻品种提供了宝贵的遗传资源。



Abstract  

The continuous rise in global temperatures and the increasing frequency of extreme heat events pose severe challenges to rice production due to heat stress. Exploring heat tolerance genes and developing heat-tolerant rice varieties represent effective strategies to address this issue. In this study, we identified a novel heat tolerance gene, OsClpI3, through analysis of the Caseinolytic proteases (Clp) ATPase gene family. OsClpI3 is predominantly expressed in leaves, encodes a chloroplast-localized protein, and positively regulates heat tolerance during both the seedling and heading stages. OsClpI3 exhibits ATPase activity, which is markedly reduced in mutant lines. Integrated transcriptomic and metabolomic analyses revealed that OsClpI3 contributes to rice thermotolerance by maintaining photosynthetic electron transport efficiency and overall photosynthetic performance under high-temperature conditions. Furthermore, natural variation in OsClpI3 affects heat tolerance, and haplotype analysis revealed a superior haplotype, Type4. These findings provide new insights into the molecular mechanisms underlying heat tolerance in rice and offer valuable genetic resources for breeding heat-tolerant rice varieties.

Keywords:  OsClpI3        heat tolerance       photosynthesis       superior haplotype       rice  
Online: 10 March 2026  
Fund: 

This work was partly granted from the National Natural Science Foundation (32401801), the Natural Science Foundation of Wuhan University of Bioengineering, China (2024KQ07), the Open Research Fund of State Key Laboratory of Hybrid Rice (Wuhan University), China (KF202502) and the Scientific and Technological Research Project of Hubei Provincial Department of Education, China (B2024293).

About author:  #Correspondence Mingxing Cheng, E-mail: chengmingxing@whu.edu.cn; Shaoqing Li, E-mail: shaoqingli@whu.edu.cn; Fengfeng Fan, E-mail: fanfengfeng@whu.edu.cn * These authors contributed equally to this work.

Cite this article: 

Fengfeng Fan, Zihan Yang, Huanran Yuan, Ayaz Ahmad, Kai Lv, Fei Xu, Manman Liu, Yu Guo, Fengfeng Si, Nengwu Li, Shaoqing Li, Mingxing Cheng. 2026. A Caseinolytic proteases ATPase family gene OsClpI3 contributes to thermotolerance in rice. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.03.017

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