Grapevine is a commercially important fruit crop cultivated for the production of table grapes, juice, wine, distilled liquors and dry raisins. In addition to its high economic value, wine is now considered a key source of health-promoting secondary metabolites, especially antioxidant polyphenols such as resveratrol. The economic importance of grapevine has encouraged many researchers to study the physiological and molecular basis of berry development, particularly those processes that affect wine quality. The availability of high-throughput analysis methods and a high-quality draft of the grapevine genome sequence has led to the characterization of berry development at the levels of the transcriptome, proteome and metabolome.We investigated berry development and withering in Vitis vinifera cv Corvina at the transcriptomic, proteomic and metabolomic levels. Transcriptomic, proteomic and metabolomic data were integrated using two different strategies, one hypothesis-free and the other hypothesis-driven. A multistep hypothesis-free approach was applied to data allowing the identification of stage-specific functional networks of linked transcripts, proteins and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data of the withering samples, starting with sub-datasets of transcripts, proteins and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time, and used these to select sub-datasets of variables. We also report here grape berry transcriptome reprogramming under the effect of common agronomical practices which affect berry repining.
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