Transcriptome of apple cv. Ametyst in Rvi6 -effective and Rvi6 -breaking Venturia inaequalis interactions identifies defense candidates
Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
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.
Highlights
• Distinct host–isolate responses were resolved in one apple genotype.
• 151 Rin-induced defense candidates, 92 in one co-expression module.
• Candidate genes are targets for future genetic validation, not yet markers.
