## 2 Results
### Targeted and Untargeted Molecular Responses: Comparison of DYE-Treated versus Untreated Berries
Consistently, a synergic co-regulation of ethylene-related genes could be evidenced, with the upregulation of a gene encoding the ethylene-forming enzyme ACO4 (_Vitvi10g02409_, group 1) [55] as well as various ERF transcription factors encoding genes, showing homology to ERF4 (_Vitvi13g01784_, group 1) (ethylene and JA inducible) [59], ERF5 (_Vitvi16g01438_, group 1) (a positive regulator of JA / ethylene response genes to enhance resistance to Botytis) [56; 57], ERF9 (_Vit12g00274_, group 1) (regulating defense mechanisms against necrotic fungi through the ethylene/JA signaling pathway), ERF105 (_Vitvi16g01444_, _Vitvi17g00787_, _Vitvi16g01434_, _Vitvi16g01432_, _Vitvi18g00295_ and _Vitvi16g01423_, group 1) (replicator of cold responses) [66], and ERF71 (_Vitvi07g00357_, group 1) (hypoxia responsive) [62]. In addition, a phosphatase (AP2C1) (_Vitvi06g00667_, group 1) negatively regulating the ethylene signaling kinases MPK4 and MPK6 [60] and two hypoxia-inducible WRKY-encoding genes (WRKY22 (_Vitvi15g01090_, group 1) and WRKY33 (_Vitvi08g00793_, group 1)) [63; 64; 65] were upregulated. The DYE treatment also displayed effects on ABA biosynthetic and signaling genes, triggering the upregulation of ABA responsive genes such as a LEA encoding gene (_Vitvi15g01084_, group 1) [75], a cystatin gene (_Vitvi18g03100_, group 1) [79], a DREB subfamily A-1 of the ERF/AP2 transcription factor gene (CBF3) (_Vitvi16g00941_, group 1), and a sulphate transporter gene (_Vitvi05g00548_, group 1) required for the activity of the ABA biosynthetic enzyme aldehyde oxidase [78], a receptor-like kinase gene (LRK10) (_Vitvi01g00353_, group 2) [80], and an SNF1-related kinase (_Vitvi17g00116_, group 1) [67] positively regulate ABA responses. Further positive regulators of ABA signaling that were upregulated by DYE treatment included a gene encoding a WRKY6 (_Vitvi10g00063_, group 1) [79], and a cysteine  
1) [73] and a WRKY44 transcription factor (_Vitvi08g00793_, group 1) [69], and an NCED4 carotenoid cleavage dioxygenase (_Vitvi02g01288_, group 2), the latter probably not involved in the direct generation of ABA [77], as well as a cytokinin responsive factor that was claimed to play a role in nitrogen uptake [93]. On the other hand, genes encoding a putative ABA biosynthetic enzyme NCED6 (_Vitvi05g00963_, group 3) [83], the ABA transporter ABCG25 (_Vitvi18g01703_, group 3) required for fine-tuning ABA export from cells, the ABA importer ABCG40 (_Vitvi04g00423_, group 3) [82], and the ABA antagonistic and gibberellin inducible gene GASA6 (_Vitvi17g00601_, group 3) [84], as well as a gene encoding a cytokinin receptor histidine kinase (_Vitvi12g00685_, group 4), a negative regulator of ABA sensitivity, were downregulated by DYE treatment. Finally, DYE treatment resulted in the overall downregulation, in comparison to untreated berries, of a gene encoding an AUX1 auxin influx carrier (_Vitvi13g00019_, group 4) [90] and one gene encoding a PIN1 auxin efflux carrier (_Vitvi17g00210_, group 3) [94], and in the upregulation of an Aux/IAA encoding gene (AUX/IAA7) (_Vitvi11g00394_, group 2) [86] and a Ca\({}^{2+}\)-dependent transducer of auxin responses (_Vitvi12g00594_, group 1) [87]. The most relevant functional results of the untargeted molecular analysis of genes listed in Table 1 are schematically represented in Figure 9. Overall, DYE treatment actively changed the expression (down and/or upregulated) of genes participating in sulphur and glutathione metabolism, plant-pathogen interaction, ROS signaling, hormone biosynthesis and signal transduction, and hormone transporters. Figure 9: Schematic overview of the transcriptional effects of DYE treatment during berry ripening, determined with KEGG analysis. Highlighting of genes in blue and blue arrows indicates downregulation, while genes and arrows marked in red indicate upregulation. Sulphur/glutathione (GSH) metabolism: APS, adenosine 5\({}^{\prime}\)-phosphosulfate.