Single-Cell and Spatial Transcriptomics in Plants: From Cell States to Inter-Tissue Coordination

Plant development and physiological responses emerge from coordinated interactions between tissues, ensuring that cell behaviors, such as division, differentiation, and environmental responses, are integrated at the organ scale. This integration is critical because plant cells are constrained by cell walls, making tissue context a key determinant of cell state and function. Classical genetics and reporters have identified mobile signals and mechanochemical feedbacks that mediate cell-cell communication, but do not provide a framework to observe how regulatory states are organized across tissue interfaces or how responses initiate, spread, and stabilize. Here, we propose that single-cell and spatial transcriptomics make inter-tissue coordination experimentally tractable by enabling measurement of transcriptional states within their tissue context, allowing researchers to investigate how regulatory information is transmitted, interpreted, and coordinated between tissues. These approaches are poised to shift the field from pathway-by-pathway models toward measurable, systems-level principles of coordination. In this review, we highlight root hormone signaling, regeneration competence domains, and immune relay networks as case studies where single-cell and spatial transcriptomics reveal coordination principles. We then define measurable features of coordinated regulatory interactions between tissues, and discuss how single-cell and spatial tools are advancing a mechanistic understanding of multicellular plant development and dynamic physiological responses.