Integrated Metabolomic and Transcriptomic Analysis Reveals the Mechanism of Dappled Fruit Formation in Hop Stunt Viroid-Infected Sweet Cherry

Sweet cherry ( Prunus avium) is a commercially vital fruit crop in China. Hop stunt viroid (HSVd) infection in sweet cherry causes dappled fruit. This study investigated the mechanism of dappled fruit formation in HSVd-infected sweet cherry using integrated metabolomics and transcriptomics. Dappled and non-dappled peel tissues were sampled at the color change and ripening stages. Ultra-performance liquid chromatography-tandem mass spectrometry identified 181 flavonoid metabolites, with peonidin-3-O-rutinoside, cyanidin-3-O-glucoside, peonidin-3-O-glucoside, cyanidin-3-O-arabinoside, cyanidin 3-xyloside, and cinchonain Ic being significantly enriched in dappled areas. RNA-seq revealed 3,287 differentially expressed genes, with PaCHS, PaCHI, PaDFR, and PaANS upregulated in dappled areas at the early stage, correlating with anthocyanin accumulation. KEGG enrichment highlighted anthocyanin and flavonoid biosynthesis pathways as central to pigmentation. This study suggests that HSVd disrupts anthocyanin biosynthesis to induce dappled pigmentation, offering novel insights into viroid–host interactions affecting fruit color in sweet cherry.