Integrated Transcriptomic and Physiological Analyses Reveal Key Genes and Regulatory Network for Early-Stage Defense Against Bacterial Fruit Blotch in Melon

Bacterial fruit blotch (BFB), caused by Acidovorax citrulli (Aac), is a devastating bacterial disease to the melon industry. The scarcity of resistant germplasms has hindered in-depth research into its resistance mechanisms. In this study, we combined comparative transcriptomics, physiological assays, and hormonal profiling to explore the defense mechanisms of resistant (ZT145) and susceptible (ZT146) melon germplasms. The results indicated that resistant plants rapidly initiated a coordinated defense mechanism within 12 h after inoculation. This was characterized by an induced increase in salicylic acid (SA), activation of core immune pathways (plant–pathogen interaction, MAPK signaling pathway, etc.), and upregulation of phenylpropanoids and other biosynthetic processes. In contrast, susceptible plants exhibited a delayed and less coordinated response, characterized by SA inhibition, a surge in jasmonic acid (JA), and the broad but non-coordinated activation of multiple pathways, ultimately leading to physiological dysregulation. Through comparative analysis, we identified nine key genes that were early responders to pathogen challenge, as well as 21 genes that might be responsible for maintaining resistance. Our findings suggest that the resistance of melon to BFB is determined not by the abundance of defense-related genes but rather by the plant’s ability to rapidly activate a coordinated, SA-dominated defense network during early infection. This study provides an integrative theoretical framework for deciphering the molecular and physiological mechanisms against bacterial diseases in melon.