P-441 - Multiplexed spatial co-profiling of plant gene expression and microbial dynamics in whole-mount tissues with PHYTOMap

The plant holobiont is a complex system shaped by dynamic interactions between plants and microbes, which range from beneficial mutualism to harmful pathogenicity. Understanding the molecular basis of the plant holobiont remains challenging due to the high heterogeneity of plant cell type-specific responses and the uneven distribution of associated microbes. While recent single-cell and spatial omics technologies provide means to analyse cellular responses at high resolution, most methods rely on thin tissue sections or require tissue dissociation, limiting a comprehensive 3D resolution of cellular diversity. PHYTOMap (Plant Hybridization-based Targeted Observation of Gene Expression Map), based on multiplexed fluorescence in situ hybridization, offers a transgene-free, cost-effective method for spatially mapping gene expression in whole-mount plant tissue. This method has been successfully applied in analysing dozens of cell-type marker genes in Arabidopsis root tips. Here, we present our ongoing efforts to expand PHYTOMap to profile microbial dynamics within whole-mount roots and to adapt for broader applicability across various plant tissues. These advancements provide powerful tools for capturing spatiotemporal information on both host gene expression and associated microbes, opening opportunities to study the crosstalk between plants and microbes at unprecedented resolution.