Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots

Ting Wang, Fanhua Wang, Shuhan Deng, Kailai Wang, Dan Feng, Fan Xu, Weijun Guo, Jia Yu, Yue Wu, Hada Wuriyanghan, Shang-Tong Li, Xiaofeng Gu, Liang Le () and Li Pu ()
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Ting Wang: Chinese Academy of Agricultural Sciences
Fanhua Wang: Chinese Academy of Agricultural Sciences
Shuhan Deng: Ltd
Kailai Wang: Ltd
Dan Feng: Chinese Academy of Agricultural Sciences
Fan Xu: Chinese Academy of Agricultural Sciences
Weijun Guo: Chinese Academy of Agricultural Sciences
Jia Yu: Chinese Academy of Agricultural Sciences
Yue Wu: Chinese Academy of Agricultural Sciences
Hada Wuriyanghan: Inner Mongolia University
Shang-Tong Li: Ltd
Xiaofeng Gu: Chinese Academy of Agricultural Sciences
Liang Le: Chinese Academy of Agricultural Sciences
Li Pu: Chinese Academy of Agricultural Sciences

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

Abstract: Abstract Plant roots perceive heat stress (HS) and adapt their architecture accordingly, which in turn influence the yield in crops. Investigating their heterogeneity and cell type-specific response to HS is essential for improving crop resilience. Here, we generate single-cell transcriptional landscape of maize (Zea mays) roots in response to HS. We characterize 15 cell clusters corresponding to 9 major cell types and identify cortex as the main root cell type responsive to HS with the most differentially expressed genes and its trajectory being preferentially affected upon HS. We find that cortex size strongly correlated with heat tolerance that is experimentally validated by using inbred lines and genetic mutation analysis of one candidate gene in maize, providing potential HS tolerance indicator and targets for crop improvement. Moreover, interspecies comparison reveals conserved root cell types and core markers in response to HS in plants, which are experimentally validated. These results provide a universal atlas for unraveling the transcriptional programs that specify and maintain the cell identity of maize roots in response to HS at a cell type-specific level.

Date: 2025
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DOI: 10.1038/s41467-024-55485-3

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