Single-cell RNA sequencing profiling cellular responses to Dickeya dadantii infection in sweet potato root tips

Abstract Bacterial stem and root rot (BSRR), triggered by Dickeya dadantii, severely reduces sweetpotato productivity, yet the cellular mechanisms underlying root responses remain poorly understood. Here, we generated a single-cell transcriptomic landscape of 40 345 cells from infected and control sweetpotato root tips to uncover cell-type-specific defense patterns. Using canonical marker genes, we delineated seven major cell types and 16 transcriptionally distinct clusters. Cortex cells were identified as the principal responders to infection, characterized by extensive transcriptional reprogramming and enriched defense-related trajectories. Among the differentially expressed genes, IbWRKY40 emerged as a core regulator within the co-expression network of root immune responses. IbWRKY40 predominantly localized to the nucleus and exhibited strong induction approximately 9 h after pathogen exposure. Functional validation in sweet potato further suggested that IbWRKY40 negatively modulates resistance to D. dadantii. To our knowledge, this is the first report elucidating the cellular-level molecular mechanisms of sweet potato root tips in response to BSRR infection, providing valuable insights into plant defense strategies under pathogen stress.