Deciphering plant–pathogen interaction with single‐cell omics

Abstract Plants are persistently exposed to a broad spectrum of pathogens, such as bacteria, fungi, oomycetes, and viruses, throughout their life cycle. Upon infection, plants activate defense‐related genes to limit damage and preserve reproductive fitness. In recent decades, most studies focused on elucidating plant immune responses at tissue or systemic level, whereas the cell‐type‐specific regulatory dynamics and cell heterogeneity during infection remain poorly understood due to methodological constraints. Recent advances in single‐cell omics have facilitated the precise decoding of cell heterogeneity during pathogen challenges. This review summarizes the technological developments in plant single‐cell omics and highlights their unique advantages for investigating nearly all stages of plant–pathogen interactions. From initial pathogen infection to the onset of local and systemic host resistance, single‐cell omics enables the identification of susceptible cell types, the discovery of cell‐type‐specific immune responses, the dissection of intercellular communication during pathogen invasion, the analysis of pathogen‐induced cell differentiation trajectories, and the spatial mapping of immune responses, with these details that are often masked in bulk analyses. By precisely capturing cellular dynamics and developmental trajectories in infected hosts, single‐cell omics is profoundly reshaping our understanding of plant–pathogen interactions. Furthermore, we propose a potential strategy for breeding crop varieties with cell‐type‐specific resistance.