Single-Cell Transcriptomic Profiling Reveals the Temporal Dynamics of Early Defense Mechanisms in Grapevine Response to Powdery Mildew Infection

Abstract

The powdery mildew pathogen Erysiphe necator poses a major threat to global viticulture, yet the earliest hours of colonization remain transcriptionally uncharacterized at the single-cell resolution. Here, we constructed a single-cell leaf transcriptomic atlas of Vitis vinifera during early E. necator infection by profiling 113,346 cells across five leaf cell types at 0-, 3-, 6-, and 12 h post-inoculation. This revealed cell-type-specific temporal dynamics of defense-related gene expression, with epidermal cells showing delayed transcriptional activation relative to other cell types. Pseudotime trajectory analysis identified four sequential transcriptional states in epidermal cells, and co-expression network analysis uncovered defense-associated gene modules. We identified 230 NLR immune receptor genes exhibiting distinct cell-type-specific expression patterns and 20 small secreted peptide (SSP)-encoding genes differentially expressed in epidermal cells, including four candidates upregulated at 3 or 6 hpi. These findings provide a transcriptomic framework for understanding cell-type-specific defense dynamics and prioritizing candidate genes for functional studies, thereby offering a molecular resource for breeding powdery mildew-resistant grapevine cultivars.