Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco

Abstract Plant–microbe interactions are essential for plant health, yet the genetic basis of host control over root-associated microbiome assembly in Nicotiana tabacum remains unclear. We integrated whole-genome resequencing, amplicon sequencing, and metabolomics across 50 tobacco cultivars, together with microbial genome-wide association and mediation analyses, to investigate host–microbiome covariation. Host genotype significantly influenced the diversity and composition of root-associated microbial communities, particularly in the rhizosphere. Several host loci were associated with heritable microbial taxa linked to nutrient acquisition and stress responses. Mediation analysis suggested that associations between host genetic variation and Pseudomonadaceae abundance were partly transmitted through secondary metabolite variation, particularly terpenoids, whereas this mediating effect was less pronounced for other taxa. Functional assays further showed that several genotype-associated bacterial isolates antagonized Fusarium oxysporum. Among them, Pseudomonas aeruginosa FZ1 suppressed pathogen growth, enhanced host defense responses, and reduced disease severity in greenhouse experiments. These findings suggest that host genetic variation is associated with shifts in the tobacco root microbiome and that secondary metabolites may contribute to the assembly of specific microbial taxa. The study provides a basis for future mechanistic and breeding-oriented investigations of microbiome-associated traits.