Transcriptomic changes in tomato plants infected with ToBRFV after cold air glow discharge plasma treatment

Abstract

Tomato brown rugose fruit virus (ToBRFV) is an emerging tobamovirus that poses a serious threat to global tomato production. In this study, we evaluated the potential of cold air glow discharge plasma (CAGDP) as a seed treatment to mitigate ToBRFV infection and induce systemic resistance in tomato plants. RNA-Seq analysis of ToBRFV-infected leaves from CAGDP-treated and untreated plants revealed significant transcriptional reprogramming. Compared to infected controls, CAGDP treatment led to the downregulation of 1237 and upregulation of 470 transcripts (|fold change| > 2, FDR < 0.05). Gene ontology (GO) enrichment highlighted the involvement of differentially expressed genes (DEGs) in oxidation-reduction processes, metabolic pathways, and defense-related cellular components. KEGG pathway analysis further indicated activation of key defense mechanisms, including plant-pathogen interaction, MAPK signaling, hormone signal transduction, and biosynthesis of secondary metabolites. Notably, CAGDP treatment enhanced the expression of genes associated with antioxidant activity and antiviral responses, while suppressing several uncharacterized and stress-related transcripts, including members of the HSP20 and nodulin-like families. RT-qPCR validation confirmed the reliability of RNA-seq data. Collectively, our findings demonstrate that CAGDP not only reduces viral accumulation but also primes the plant’s immune system through coordinated transcriptomic shifts. This study provides a molecular foundation for using non-thermal plasma as a sustainable strategy to manage ToBRFV and potentially other viral diseases in crops.