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

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.