Transcriptome of apple cv. Ametyst in Rvi6-effective and Rvi6-breaking Venturia inaequalis interactions identifies defense candidates

Background: Rvi6, introgressed from Malus floribunda 821, is the most widely deployed apple scab resistance gene, but Venturia inaequalis races overcoming it are widespread. Transcriptomic differences between Rvi6-effective and Rvi6-breaking interactions in one host genotype remain unresolved. Aims: To compare these interactions in cv. Ametyst and nominate genes for subsequent validation. Methods: Own-rooted Ametyst plants were mock-inoculated or inoculated with an Rvi6-avirulent isolate (Rin; incompatible) or an Rvi6-virulent isolate (Rola; compatible) and harvested at 4 days post-inoculation (21 mRNA libraries). Expression was quantified using GDDH13 reference-based and de novo Trinity strategies, followed by DESeq2, WGCNA and GSEA. Results: Rin vs Rola yielded 1,339 candidate genes (more than two-fold change, FDR < 0.01) in the reference-based analysis. Curation of Rin-induced defense candidates retained 151 genes, 92 of which concentrated in a single co-expression module. Thirty-one also passed the Rin-vs-Rola thresholded test and were prioritized for genetic validation. Conclusions: The incompatible interaction was associated with a coherent defense program and the compatible interaction with a distinct transcriptional state. With one isolate per class, isolate identity and Rvi6 virulence cannot be separated.