Dissecting the Cell‐Type‐Specific Response to an Emerging Tobamovirus in Tomato Reveals Cultivar‐Dependent Involvement of Brassinosteroid Signalling

Plant viruses drive widespread crop epidemics, yet the host plant responses across different cell types, particularly how these responses are influenced by cultivars with varying genetic backgrounds, including the presence of resistance (R) genes, remain poorly understood. Using tomato brown rugose fruit virus (ToBRFV) and two tomato cultivars, 'Jinpeng No. 1' (JP) and 'Rutgers' (RG), with different genetic backgrounds, this study used single-cell RNA sequencing to explore infection dynamics and responses at the cellular level. Results showed that ToBRFV accumulated to different levels in the two cultivars, likely due to differences in their genetic backgrounds, particularly the distinct genotypes of the Tm-2² and tm-2 alleles. Following infection, the composition of cell types in tomato leaves also varied between the two cultivars. While the entry or movement of ToBRFV in the JP cultivar was not fully prevented early on, the viral accumulation in certain cell types of this cultivar was restricted. ToBRFV alters signalling pathways based on cell type and cultivars. Pseudotime analysis revealed that, in JP plants, ToBRFV reverses expression of brassinosteroid (BR) positive regulators during mesophyll cell development. Silencing positive BR regulators increased infection in JP plants, while suppressing it in RG plants, linking BR signalling to JP-dependent resistance. Exogenous BR suppressed ToBRFV in JP but enhanced it in RG plants. This study reveals the differential involvement of BR signalling during viral infection in the two cultivars, offering a framework for future studies of plant-virus interactions.