Single-nucleus transcriptomic profiling reveals cell type-specific responses of the soybean root tip to aluminum...

Aluminum (Al) toxicity resulting from soil acidification poses a major constraint on crop productivity. Although the root apex serves as the primary site for Al perception and adaptive remodeling, cell type-resolved responses to prolonged Al exposure remain poorly characterized. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to generate a cell type-resolved transcriptomic atlas of the soybean (Glycine max) root tip under Al stress. We profiled a total of 79,201 high-quality nuclei and identified nine major root cell types. Our results reveal that Al stress elicits shared transcriptional responses across cell types while reshaping root cell type composition. Notably, the proportion of nuclei increased in the epidermal cell layer (from 34.16% to 70.41%). In contrast, a significant reduction in nuclear number was detected within the cortical cells (from 40.70% to 8.53%). Interestingly, microscopic examination further indicated a pronounced expansion of regions exhibiting patterns inconsistent with the decrease in cortical nuclei. Cell type-specific analyses identified a total of 20,544 differentially expressed genes (DEGs) and showed that epidermal cells primarily responded to Al stress by activating transcriptional programs associated with transport, cell wall reinforcement, and defense, accompanied by enhanced fatty acid biosynthesis and cuticle-related pathways. In contrast, cortical cells exhibited repression of cell cycle-related transcriptional programs, consistent with their reduced cell abundance and indicating that limitations in cell division are closely associated with cortical cell loss. Furthermore, untargeted metabolomic profiling supported an important role of lipid metabolism in the response to Al stress. Collectively, our study reveals cell type-specific response patterns of the soybean root tip to long-term Al stress at single-nucleus resolution and provides new insights into the cellular mechanisms underlying aluminum tolerance in crop roots.