GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE345nnn/GSE345841/primaryOK200TranscriptomicsMalus domesticaExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE345841GEOGSEfalseTranscriptomic response of apple cv. Ametyst to virulent and avirulent Venturia inaequalis identifies Rin-induced defense candidatesRvi6, introgressed from Malus floribunda 821, is the most widely deployed scab resistance gene in apple, yet Venturia inaequalis isolates able to overcome it are now widespread. How an Rvi6-effective interaction differs transcriptomically from an Rvi6-breaking interaction in the same host genotype has remained unresolved. Own-rooted plants of cv. Ametyst, which carries Rvi6, were inoculated with an avirulent isolate (Rin, from 'Rubin'), a virulent isolate (Rola, from 'Rubinola'), or a distilled-water mock, and leaves were harvested 4 days post-inoculation, giving 21 mRNA libraries. Expression was quantified with two complementary strategies, GDDH13 reference-based and de novo Trinity, followed by differential expression analysis with DESeq2, weighted gene co-expression network analysis and gene-set enrichment analysis. The Rin-versus-Rola contrast yielded 1,339 thresholded-Wald candidates in the reference-based layer; curation of defense-annotated Rin-induced candidates gave 151 genes, 92 of which concentrated in a single co-expression module. The incompatible interaction was associated with a coherent defense program, whereas the compatible interaction showed a distinct transcriptional state.2026/09/02GSE345841GSM10017747GSM10017736GSM10017748GSM10017737GSM10017738GSM10017749GSM10017739GSM10017754GSM10017743GSM10017744GSM10017745GSM10017734GSM10017735GSM10017746GSM10017750GSM10017751GSM10017740GSM10017752GSM10017741GSM10017742GSM1001775329987345841Malus domestica