title: Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars.
abstract: BACKGROUND
  Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems.
  
  
  RESULTS
  Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity (°Brix-to-titratable acidity ratio) from the same experimental vineyard. The cultivars were exposed to a mild, seasonal water-deficit treatment from fruit set until harvest in 2011. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNAseq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. The mild water deficit treatment did not significantly alter the abundance of proteins or metabolites measured in the five cultivars, but did have a small effect on gene expression.
  
  
  CONCLUSIONS
  The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA. rghan@nevada.unr.edu.
authors.forename: Ryan
authors.initials: R
authors.lastname: Ghan
authors.affiliation: Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia. steve.vansluyter@mq.edu.au.
authors.forename: Steven C
authors.initials: SC
authors.lastname: Van Sluyter
authors.affiliation: Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel. uriho9842@yahoo.com.
authors.forename: Uri
authors.initials: U
authors.lastname: Hochberg
authors.affiliation: Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel. degua3@gmail.com.
authors.forename: Asfaw
authors.initials: A
authors.lastname: Degu
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA. dwilliamhopper@nevada.unr.edu.
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Hopper
authors.affiliation: Nevada Center for Bioinformatics, University of Nevada, Reno, Reno, NV, 89557, USA. rltillett@unr.edu.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Tillet
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA. schlauch@unr.edu.|Nevada Center for Bioinformatics, University of Nevada, Reno, Reno, NV, 89557, USA. schlauch@unr.edu.
authors.forename: Karen A
authors.initials: KA
authors.lastname: Schlauch
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia. paul.haynes@mq.edu.au.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Haynes
authors.affiliation: Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel. fait@bgu.ac.il.
authors.forename: Aaron
authors.initials: A
authors.lastname: Fait
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA. cramer@unr.edu.
authors.forename: Grant R
authors.initials: GR
authors.lastname: Cramer
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000872:Anthocyanins / Q000096:biosynthesis; D019295:Computational Biology; D005638:Fruit / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling; D055432:Metabolomics; D020005:Propanols / Q000378:metabolism; D040901:Proteomics; D027843:Vitis / Q000235:genetics* / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D000872:Anthocyanins; D020005:Propanols; C439395:1-phenylpropanol