Transcriptomic analysis reveals lignin-associated genes involved in ToBRFV-induced brown hardened spots and defense in tomato fruit

Tomato brown rugose fruit virus (ToBRFV) represents a significant threat to global tomato production, resulting in decreased yields and compromised fruit quality due to the formation of brown, hardened spots on infected fruit. This study aimed to elucidate the molecular mechanisms for ToBRFV-induced lesions in tomato fruit using transcriptome sequencing and virus-induced gene silencing (VIGS) techniques. Transcriptome analysis was conducted on tomato fruit at green-ripe (L), and red-ripe (H) stages, examining three tissue types: brown lesions (B), non-brown areas of infected fruit (BC), and healthy controls (CK). A total of 34 differentially expressed genes (DEGs) related to phenylpropanoid biosynthesis were identified, with PAL (Solyc05g056170.3), C4H (Solyc05g047530.3), CAD (Solyc02g069250.3), and POD (Solyc02g094180.3) showing the highest transcript abundances in brown lesion tissues. Crucially, silencing POD (Solyc02g094180.3) increased tomato susceptibility to ToBRFV, accompanied by increased accumulation of hydrogen peroxide (H2O2), and superoxide anions (O2•−). In contrast, silencing PAL (Solyc05g056170.3), C4H (Solyc05g047530.3), or CAD (Solyc02g069250.3) improved resistance and suppressed viral accumulation. Collectively, these findings indicate that these four genes are crucial regulators of lignin biosynthesis in tomato, and that the brown hardened lesions induced by ToBRFV are associated with lignin accumulation. Furthermore, POD plays a vital role in mediating resistance to ToBRFV by regulating reactive oxygen species. This study provides important insights into the molecular responses of tomato fruit, laying a foundation for breeding ToBRFV-resistant tomato varieties with improved fruit quality.