Mechanistic Basis of Trichoderma-Mediated Systemic Resistance Against Fusarium Crown Rot in Tomato: A Multi-Omics Investigation in North West Nigeria

Trichoderma spp. are well-established biological control agents against soilborne pathogens, yet the mechanistic basis by which Trichoderma-root interactions trigger systemic resistance against vascular and crown rot pathogens under tropical field conditions remains incompletely understood. Understanding these mechanisms at the molecular level is essential for optimising biocontrol formulation, application timing, and integration with other management strategies. This doctoral research employs a multi-omics approach to elucidate the systemic resistance mechanisms induced by Trichoderma asperellum TRI-KN12, an elite indigenous isolate characterised in preliminary screening from Kano State irrigated tomato soils, against Fusarium oxysporum f. sp. radicis-lycopersici crown and root rot. Transcriptomic profiling of tomato roots and shoots at 24, 72, and 168 hours post-Trichoderma colonisation, before and after Fusarium challenge, is conducted using RNA-seq, with differentially expressed gene analysis focusing on salicylate, jasmonate, and ethylene defence pathways. Metabolomic profiling of root exudates and systemic secondary metabolites is performed using liquid chromatography-mass spectrometry. Proteomic analysis targets pathogenesis-related protein accumulation in Trichoderma-treated versus control plants following pathogen challenge. Field trials across three growing seasons validate that TRI-KN12 application provides commercially relevant disease suppression under North West Nigerian field conditions, linking mechanistic laboratory findings to applied outcomes. The research produces the first multi-omics characterisation of Trichoderma-induced systemic resistance under West African tropical conditions, with direct implications for biocontrol product development. Keywords: Trichoderma, systemic resistance, Fusarium crown rot, multi-omics, tomato.