Integrated multi-omics analysis of resistant and susceptible Brassica napus roots reveals phenylpropanoid biosynthesis associated with clubroot resistance

Clubroot is a soil-borne disease caused by the obligate biotrophic pathogen Plasmodiophora brassicae, severely affecting cruciferous crops worldwide, especially Brassica napus. However, cultivar-dependent features associated with contrasting clubroot phenotypes under natural field conditions remain poorly understood. To investigate these multi-omics features at the late disease stage, an integrated transcriptomic, untargeted metabolomic, and root endophytic microbiome analysis was performed using resistant and susceptible B. napus cultivars collected from a naturally infested field. Comparative analysis revealed significant multi-omics differences between the two cultivars. Among the enriched pathways, phenylpropanoid biosynthesis was identified as a major resistance-associated feature, supported by the upregulation of multiple structural genes involved in lignin and phenolic compound biosynthesis, including PAL, 4CL, CCR, POD, CAD, and F5H, together with the increased accumulation of phenylpropanoid-related metabolites such as Caffeic acid, Coniferyl aldehyde, and Sinapyl alcohol. In addition, resistant roots showed elevated levels of glucosinolate-derived metabolites, particularly isothiocyanate-related compounds. Hormone signaling-related genes, especially those associated with jasmonate and auxin pathways, also displayed differential expression patterns between resistant and susceptible cultivars and were further supported by RT-qPCR validation. Microbiome analysis further revealed differences in root endophytic bacterial community composition between the two cultivars, with several bacterial genera showing positive correlations with metabolites enriched in resistant roots. Overall, these findings reveal cultivar-dependent multi-omics differences accompanying contrasting clubroot phenotypes under natural field infection conditions and provide a basis for future studies of clubroot resistance in B. napus.