Single‐Nucleus Transcriptomics Reveals Cell Type Specific Defence Responses and Identifies AhWRKY40 as a Key Regulator of Peanut Resistance to Sclerotium rolfsii

Peanut stem rot caused by Sclerotium rolfsii is a devastating soil borne disease that severely constrains peanut production worldwide. Despite its economic importance, highly resistant peanut cultivars are still largely unavailable, and the cellular and molecular mechanisms underlying peanut resistance remain poorly understood. We obtained a total of 29,308 high-quality nuclei, annotated five major cell types, and detected 52,819 expressed genes. Comparative analysis revealed widespread transcriptional reprogramming and a predominance of downregulated genes in response to pathogen infection, accompanied by a substantial reduction in cell abundance across all cell populations. Notably, epidermal cells harboured the highest proportion of disease resistance genes. Pseudotime trajectory analysis further demonstrated that S. rolfsii infection altered cellular transcriptional states and induced cell type specific immune reprogramming. Integrative analyses combining gene coexpression, pseudotime dynamics, virtual knockout, and transgenic validation consistently identified AhWRKY40 as a key regulatory factor associated with disease resistance. Overexpression of AhWRKY40 enhanced resistance to S. rolfsii and was accompanied by increased accumulation of jasmonic acid (JA) and salicylic acid (SA), suggesting its involvement in hormone-mediated defence responses. Collectively, our study provides new insights into the cellular and molecular mechanisms underlying peanut resistance to stem rot, identifies AhWRKY40 as a promising candidate gene for disease resistance, and establishes a valuable resource for functional genomics and molecular breeding to improve southern blight resistance in peanut.