Pathogenic variability of Thielaviopsis paradoxa and differential transcriptomic responses of Oil palm cultivars to isolates of contrasting virulence

Thielaviopsis paradoxa is a widespread soil-borne fungus and a major pathogen of oil palm, responsible for substantial yield losses worldwide. Understanding host–pathogen interactions is critical for developing resistant cultivars. In this study, we examined the pathogenicity and transcriptomic responses of two oil palm cultivars, Tenera and Malaysian Dwarf, following inoculation with 11 T. paradoxa isolates, including the highly virulent DA002 and the low-virulence AA034. Pathogenicity assays revealed strong isolate- and cultivar-dependent disease outcomes: Tenera was highly susceptible to DA002, displaying chlorosis, spear collapse, and tissue necrosis, whereas Malaysian Dwarf remained asymptomatic with both isolates, reflecting enhanced tolerance. Transcriptome profiling identified 2,093 and 1,577 differentially expressed genes (DEGs) in Tenera and Malaysian Dwarf, respectively, following DA002 infection, compared with 1,130 and 244 DEGs after AA034 infection. Tenera mounted a broad but energetically costly defense, characterized by mixed regulation of PR proteins, R-gene homologs, receptor-like kinases, oxidative enzymes, and phenylpropanoid, flavonoid, and lignin biosynthesis genes. In contrast, Malaysian Dwarf exhibited a targeted and coordinated transcriptional response, including selective activation of glutathione metabolism and antioxidant enzymes to maintain redox balance, alongside efficient upregulation of secondary metabolite pathways, such as alkaloids, terpenoids, and phenylpropanoids. This integrated strategy likely underlies its asymptomatic phenotype and effective containment of pathogen colonization within the duration of the experiment. Functional enrichment analyses revealed cultivar- and isolate-specific activation of immune components, ROS detoxification, and specialized metabolism, highlighting how host genetic and physiological traits shape responses to pathogen virulence. Collectively, these findings elucidate the relationship between pathogen virulence, host transcriptional reprogramming, and cultivar-specific defense strategies, providing a molecular basis for breeding of oil palm varieties with improved disease resistance and sustainable yield performance. • Pathogenicity of Thielaviopsis paradoxa varies strongly with isolate virulence and oil palm cultivar. • The virulent isolate DA002 causes severe disease in Tenera but not in Malaysian Dwarf. • Tenera activates a broad, energetically costly defense involving PR genes, RLKs, and phenylpropanoid pathways. • Malaysian Dwarf mounts a targeted defense emphasizing redox balance and secondary metabolism. • Cultivar-specific transcriptional strategies explain tolerance and disease containment in oil palm.