Single-cell and spatial dissection of plant immune pathways

Understanding the fundamental mechanisms of plant immunity is crucial for addressing crop losses caused by diseases and to enhance agricultural resilience through breeding and engineering. The multicellular nature of plants, where each cell has unique functions influenced by changing environments, necessitates a detailed examination of the plant immune system at the single-cell level. Our recent research employing novel single-cell and spatial omics technologies has discovered that there are numerous cell populations that exhibit distinct immune responses (immune cell states), representing both cell-autonomous and non-cell-autonomous responses. The next essential phase of research will be to elucidate the function and regulation of immune cell states, defining how they communicate with each other. In particular, how well-known plant immune components and mechanisms play roles in cell-autonomous and non-cell-autonomous immune responses remains an outstanding open question. This project tackles this knowledge gap by both cellular-level and genome-wide analyses of plant immunity, focusing on two critical immune pathways: salicylic acid (SA) and systemic acquired resistance (SAR) pathways. SA is a major defence hormone produced upon pathogen recognition and contributes to various processes important for immunity. SAR includes responses of infected leaves that send signal to distal tissues to provide immune priming. The plant biology community has created extensive genetic resources, including mutants, that can dissect the contributions of SA biosynthesis and various pathways, including SAR pathways. With the multidisciplinary integration of these genetic resources and our cutting-edge single-cell and spatial omics technologies, we aim to mechanistically understand how SA and SAR pathways regulate specific immune cell states and contribute to cell-cell communications at an unprecedented scale. To achieve this goal, we will: Create an atlas of cellular states in pathogen-infected leaves using single-cell transcriptomics, epigenomics, and spatial transcriptomics in various SA- and SAR-related mutants. Experimentally validate the function and regulation of immune cell states regulated by SA and SAR pathways, identifying relevant cell states for further precision engineering and breeding strategies. Innovate a new imaging method to simultaneously measure SA accumulation and transcriptionally defined cell states at single-cell and spatial resolution, directly linking the spatial distribution of the critical plant hormone and cell state dynamics for the first time. The resulting atlas, technologies, and insights into the role of SA and SAR across different cell states will be instrumental in advancing our basic understanding of plant immunity at the cellular level. This knowledge paves the way for precision engineering of specific cell states, enabling the combination of multiple beneficial traits within a single plant. Such an approach could mark a new era in crop breeding, producing plants that are resilient to changing climates and ensuring sustainable food security. This project's multidisciplinary approach, combining genomics, cell biology, and plant pathology, fosters collaboration across scientific disciplines. The comprehensive single-cell atlas we generate will serve as a valuable resource for the broader plant science community, accelerating research in plant-microbe interactions. Furthermore, the integration of SA biosensors and insights from single-cell and spatial transcriptomics offers a new approach to studying plant-pathogen interactions. In summary, our research will provide unprecedented new insight into the cellular basis of plant immunity, develop innovative technologies, and generate valuable resources for the scientific community. These advances will contribute significantly to global food security efforts by enhancing our ability to develop crops resilient to diseases and changing environmental conditions.