Title | Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks |
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Publication Type | Articolo su Rivista peer-reviewed |
Year of Publication | 2010 |
Authors | Zamboni, A., Di Carli Mariasole, Guzzo F., Stocchero M., Zenoni S., Ferrarini A., Tononi P., Toffali K., Desiderio Angiola, Lilley K.S., Pè M.E., Benvenuto Eugenio, Delledonne M., and Pezzotti M. |
Journal | Plant Physiology |
Volume | 154 |
Pagination | 1439 - 1459 |
Date Published | 2010 |
ISBN Number | 00320889 (ISSN) |
Keywords | article, biological marker, Biological Markers, cluster analysis, DNA microarray, fruit, gene expression profiling, gene expression regulation, genetics, Genomics, grape, metabolomics, Oligonucleotide Array Sequence Analysis, Plant, plant RNA, Proteomics, RNA, Vitis, Vitis vinifera |
Abstract | The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. 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 from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified 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 from three withering intervals, starting with subdata sets 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 subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed. © 2010 American Society of Plant Biologists. |
Notes | Cited By :51Export Date: 16 July 2015CODEN: PLPHACorrespondence Address: Pezzotti, M.; Department of Biotechnology, University of Verona, 37134 Verona, Italy; email: mario.pezzotti@univr.itMolecular Sequence Numbers: GENBANK: GSE20511;Chemicals/CAS: Biological Markers; RNA, PlantReferences: Adrian, M., Jeandet, P., Veneau, J., Weston, L.A., Bessis, R., Biological activity of resveratrol, stilbenic compound from grapevine, against Botrytis cinerea, the causal agent for gray mold (1997) J Chem Ecol, 23, pp. 1689-1702;Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs (1997) Nucleic Acids Res, 25, pp. 3389-3402; Arnholdt-Schmitt, B., Stress-induced cell reprogramming: A role for global genome regulation? 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