Transcriptomic insights into the biocontrol mechanism of Trichoderma spp. against Fusarium wilt in melon

Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. melonis (FOM), is a devastating disease severely impacting global melon (Cucumis melo L.) production. Biocontrol agents such as Trichoderma species, offer a sustainable alternative to chemical fungicides, yet their precise molecular mechanisms remain underexplored. In this study, we tested the antifungal efficacy of a commercial formulation combining two Trichoderma strains (Trichoderma asperellum ICC012 and Trichoderma gamsii ICC080) against FOM and investigated the molecular mechanisms underlying the melon roots Trichoderma-induced responses. Through phenotypic screening, RNA sequencing, and a Weighted Gene Co-expression Network Analysis (WGCNA) we demonstrated that Trichoderma pre-treatment significantly mitigates FW symptoms and orchestrates a robust defense response in melon roots. Our analysis revealed specific transcriptional reprogramming, including the upregulation of key hub genes such as NAC domain-containing protein 2, dehydration-responsive element-binding protein 1A (DREB1A), trihelix transcription factor GT-3b, and a caffeoylshikimate esterase-like encoding gene involved in lignin biosynthesis. Furthermore, critical pathways significantly enriched in Trichoderma-treated roots included phenylpropanoid biosynthesis, MAPK signaling pathway, and plant-pathogen interaction, alongside defense-related processes like zeatin and tryptophan biosynthesis and ABC transporter activity. These molecular reconfigurations highlight the complex signaling networks activated by Trichoderma spp., leading to enhanced immunity against FOM. Our findings provide crucial molecular insights into Trichoderma-mediated biocontrol, elucidating specific genetic and metabolic modulations in melon roots. This research paves the way for targeted breeding strategies and advanced industrial applications of Trichoderma spp. for effective and sustainable management of Fusarium wilt in melon crops.