Transcriptomic response of apple cv. Ametyst to virulent and avirulent Venturia inaequalis identifies Rin-induced defense candidates

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.