Transcriptomic changes in tomato brown rugose fruit virus-infected tomato in response to low-dose gamma irradiation

Tomato brown rugose fruit virus (ToBRFV) is a highly destructive and rapidly spreading tobamovirus that poses a serious threat to global tomato production. While low-dose gamma irradiation has emerged as a promising non-chemical strategy to enhance host resistance, the molecular mechanisms and transcriptomic reprogramming underlying this induced resistance remain largely unexplored. In this study, we employed a transcriptome-wide RNA sequencing approach to elucidate the specific gene expression networks and defense pathways activated in ToBRFV-infected tomato plants in response to low-dose gamma irradiation, addressing a critical gap in our understanding of host-virus interactions under irradiation priming. Naturally infected tomato seeds were exposed to an optimized gamma dose of 15 Gy, and transcriptomic profiles of irradiated plants were compared with those of non-irradiated infected controls. RNA-Seq analysis identified 469 differentially expressed genes (DEGs), including 157 upregulated and 312 downregulated transcripts (FDR < 0.05), indicating that gamma irradiation induces extensive transcriptional reprogramming. Functional enrichment analyses revealed significant activation of pathways related to metabolic reorganization, antioxidant defense, plant hormone signal transduction, secondary metabolite biosynthesis, and MAPK signaling. Notably, key defense-associated genes encoding peroxidases, protein kinases, and tetratricopeptide repeat (TPR) domain-containing proteins were strongly upregulated, suggesting enhanced reactive oxygen species (ROS) detoxification, stress signal amplification, and potential restriction of viral replication. In contrast, several growth- and development-related transcription factors and heat shock proteins were markedly downregulated, reflecting a shift in resource allocation toward defense responses. Quantitative RT-PCR validation of selected hormone-related genes confirmed the reliability of the RNA-Seq data and highlighted the coordinated involvement of auxin, ethylene, and gibberellin signaling in stress adaptation. Collectively, our results provide novel molecular evidence defining how low-dose gamma irradiation primes endogenous defense networks to reduce viral accumulation. This study offers new insights into the host-mediated transcriptional regulation of resistance against ToBRFV, establishing a foundation for future functional studies on irradiation-induced immunity.