Transcriptome-hormone network analysis tentatively reveals a chalcone synthase 1-dependent pathway for tobacco mosaic virus resistance in tobacco

Tobacco mosaic virus (TMV) is one of the most widespread and common diseases in tobacco production and is extremely harmful to tobacco. Numerous studies have shown that flavonoids have a wide range of biological activities, such as UV protectors, signaling molecules in plant-microbe interactions, and antioxidants. CHS, a key phenylpropanoid pathway enzyme, catalyzes chalcone biosynthesis, which are precursors for anthocyanins and flavonols. These compounds regulate plant pigmentation and exhibit antioxidant, antiviral, and antibacterial properties. In the current study, we generated NtCHS1-overexpressing (CO) and interfering (CR) tobacco lines in HD and DBJ599 backgrounds, respectively. Transcriptome sequencing and phytohormone profiling (JA, SA, and derivatives) were performed at 0, 6, 12, 24, and 48 h post-TMV infection. Identification of 1867 specific differentially expressed genes (SDEGs), enriched in MAPK signaling, hormone transduction, and flavonoid pathways, with NAC, MYB, and WRKY transcription factors dominating the regulatory network. PCA of transcriptome data revealed three temporal clusters, with CR showing delayed responses at 48 h. Hormone analysis showed biphasic JA/SA patterns: JA declined until 24 h but rebounded at 48 h, while SA peaked at 6 h before suppression. CR exhibited reduced JA/SA compared to DBJ599, whereas CO showed SA deficiency. weighted gene correlation network analysis (WGCNA) highlights a green module that is closely linked to hormone dynamics. It contains Nitab4.5_0000662g0120, a putative hub gene in jasmonate biosynthesis, a gene that will be the focus of our future validation. The functional validation of Nitab4.5_0000662g0120 in this study remains incomplete as well as the molecular mechanism by which NtCHS1 cross-regulates SA-JA signaling has yet to be resolved. Despite these constraints, this research work deepens the understanding of flavonoid-hormone interactions in antiviral immunity and provides a roadmap for engineering anti-TMV crops through metabolic pathway modulation.