A Comparative Transcriptome and WGCNA of Tomato Reveals Hub Genes and a Hormone-Mediated Defense Network Against Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum is a major constraint on tomato (Solanum lycopersicum L.) production, yet the molecular basis of quantitative resistance remains poorly understood. In this study, comparative transcriptome profiling was performed on resistant (‘ZM3’) and susceptible (‘ZM86’) tomato inbred lines following pathogen inoculation in roots, stems, and leaves. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify resistance-associated regulatory modules and hub genes. The results revealed distinct gene expression patterns between the two genotypes after infection. Several co-expression modules were significantly associated with resistance or susceptibility traits. Functional enrichment analysis showed that differentially expressed genes were mainly involved in plant hormone signal transduction, plant–pathogen interaction, phenylpropanoid biosynthesis, and cell wall modification. Genes related to ethylene and salicylic acid signaling were strongly induced following infection, whereas brassinosteroid-associated genes showed genotype-dependent expression patterns. Network analysis further identified several hub genes within defense-related modules, including ACO (Solyc04g007980), ERF1 (Solyc09g091950), MAPK9, receptor-like kinase RLK (Solyc07g006770), and a dirigent family gene (Solyc10g008900). Taken together, our results suggest that tomato resistance to Ralstonia solanacearum involves a coordinated defense network integrating hormone-mediated transcriptional regulation and structural reinforcement, and provides candidate genes for breeding bacterial wilt-resistant cultivars.