Decoding spatial heterogeneity in plants: Advances and challenges in spatial transcriptomics for stress responses and crop resilience

• Advanced spatial barcoding achieves subcellular resolution in plants. • Maps cell-specific gene dynamics in stress, development, & symbiosis. • Rigid cell walls, vacuoles, and autofluorescence hinder application. • Plant-optimized tools aid gene discovery and breeding for resilience. Spatial omics technologies are profoundly transforming plant systems biology. By resolving the spatial information of gene expression within native tissue architecture, they provide a novel perspective for understanding plant life processes. Spatial transcriptomics is revolutionizing plant systems biology by preserving gene expression within its native tissue architecture. For sessile organisms, positional information is fundamentally linked to cell fate and physiological function. Traditional single-cell sequencing requires tissue dissociation, which severs this context, making spatial technologies essential for understanding complex regulatory networks. This review highlights how spatial resolution uncovers heterogeneous strategies for coping with environmental challenges. In abiotic stress, studies reveal cell-type-specific responses, such as metabolic reprogramming in poplar leaves during drought and cell wall remodeling in rice roots facing soil compaction. Regarding biotic stress, these technologies resolve plant pathogen interfaces, identifying localized immune responses in rice and coordinated defense modules in potato leaves. By pinpointing defensive modules in specific cell layers, researchers can transition from identifying broad responsive genes to delineating the precise cellular architects of resilience. Despite challenges like rigid cell walls and autofluorescence, advancements in high-resolution panoramic analysis and multi-omics integration are enabling the construction of virtual plant frameworks. These spatial maps transform gene lists into functional blueprints for designing next-generation crops with targeted, durable resistance to climate challenges.