Rewiring of auxin and MAPK signaling is associated with contrasting shoestring and fern-like manifestations in ToBRFV-A134T-infected tomato

Introduction – Tomato brown rugose fruit virus (ToBRFV) is a rapidly spreading plant pathogen that threatens tomato cultivation worldwide, leading to economic losses. ToBRFV-A134T, a new isolate, induces a subset of plant responses characterized by unique severe shoestring-like and fern-like manifestations. We aimed to investigate the differential host response of Tm-2²-resistant tomato plants toward ToBRFV-A134T versus the wildtype isolate (ToBRFV-WT) to understand the mechanisms underlying these distinct manifestations. Methods – We performed symptomatology analysis to follow the temporal development of shoestring and fern-like symptoms in ToBRFV-A134T-infected tomato plants. Comparative transcriptomic analysis of RNA-seq data from three biological replicates per leaf manifestation, sampled at 38 days post-inoculation, was conducted to identify differentially expressed genes and enriched pathways. In parallel, ToBRFV-WT-infected tomato plants were treated with exogenous auxin to test whether auxin perturbation could recapitulate ToBRFV-A134T-associated symptoms. Results – Shoestring symptoms consistently preceded fern-like symptoms in ToBRFV-A134T-infected plants and progressed to a mixture of manifestations at late disease stages. ToBRFV-A134T-induced shoestring symptoms were associated with a distinct subset of auxin-responsive genes and enrichment of the MAP kinase pathway. Salicylic acid-mediated defense was suppressed in shoestring leaves but remained active in fern-like leaves, as indicated by downregulation versus upregulation of Pathogenesis related-1 (PR-1) genes, respectively. Despite equivalent ToBRFV accumulation across infected phenotypes, fern-like leaves showed a transcriptional profile highly similar to that of healthy, non-infected controls. Exogenous auxin treatments of ToBRFV-WT-infected plants increased the occurrence of shoestring symptoms and recapitulated the unique fern-like manifestations induced by ToBRFV-A134T. Discussion – These findings indicate that distinct rewiring of auxin signaling, MAPK signaling, and salicylic acid-mediated defense is associated with divergent foliar manifestations of ToBRFV disease in Tm-2²-resistant tomato plants. Auxin emerges as a key determinant of symptom identity, linking hormonal crosstalk to the contrasting shoestring and fern-like outcomes observed for the ToBRFV-A134T isolate.