Progress 09/01/06 to 07/31/12
Outputs
OUTPUTS: For additional information, please contact Grant Cramer at 775-784-4204 or cramer@unr.edu PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For additional information, please contact Grant Cramer at 775-784-4204 or cramer@unr.edu
Publications
- No publications reported this period
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: In the last year, we have conducted DIGE experiments on Seyval and V. riparia buds at 42 days after exposure to long or short days. Three hundred proteins were found to be significantly different either by the genotype, treatment or genotype x treatment interaction. Proteins from two-hundred and fifty spots were identified by MALDI TOF/TOF or reconfirmed by the Thermo Scientific LTQ Orbitrap mass spectrometer, which is much more sensitive. Twenty-four additional spots were analyzed with the Thermo Scientific LTQ Orbitrap mass spectrometer. Twenty-six spots were of such low abundance that they could not be analyzed accurately. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The increased sensitivity of the Orbitrap machine determined that many spots had more than one protein, some had as high as 20 proteins in a spot. In total, approximately 750 proteins were identified in the buds. The data is still under analysis and the manuscript is being re-written to accommodate the new dataset. In separate analyses, metabolites were analyzed by GC-MS between days 1 and 42 for both treatments and genotypes. Several compounds were found to be significantly different with genotype and treatment. These compounds included some sugars, sugar alcohols and amino acids. Raffinose concentration differences were particularly interesting and appear to correlate well with the transcriptomic data.
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Major experimental projects and unpublished results to date: Bud morphology and transcriptomics: Molecular profiling (transcripts, proteins, and metabolites) of a Vitis genetic system with differences in endodormancy induction. Shoots vines (12 nodes) were exposed to short (SD) or long (LD) photoperiods to induce or inhibit endodormancy. Molecular and histological profiles were analyzed during a 42-day period of development in LD and SD. Bud development was similar in LD and SD up to 14 days of treatment and buds were floral competent by 21 days, but development of floral meristems was slowed in SD buds (manuscript submitted to Plant Molecular Biology). Transcriptomic datasets have been uploaded to GEO and PLEXdb databases. Transcriptomic analyses indicated 3,186 probesets with a significant Photoperiod*Time effect during bud development. Ontology analysis showed transcription, cell communication, and protein synthesis, binding and fate were significantly upregulated in response to SD during increased development of secondary and tertiary meristems. When buds were floral competent (21 days) there was an upregulation in SD of genes of ABA biosynthesis, fatty acid signaling, protein fate, and storage proteins. Transition to endodormancy occurred at 21 days and was fully induced at 42 days SD, which corresponded with increased ABA signaling, transcription, and protein synthesis. Of particular interest was the upregulation of NCED as buds entered endodormancy (28 to 42 days). In conjunction with this ABA HYPERSENSITIVE GERMINATION 3 (AHG3/HAB2), a protein phosphatase type 2C negative regulator of ABA signaling, was downregulated at the time that SD buds were transitioning to full endodormancy (21 to 42 days). HAB2 homologues interact functionally with histone deacetylase HD2C [158] and bind with chromatin remodeling ATPase SWI3B [159] and the recently discovered PYR ABA receptors [52, 53], making it an attractive candidate for functional characterization in grape. Bud proteomics and metabolomics: Proteomic analysis revealed 868 spots in common between Vitis genotypes. Comparison between this bud consensus map and a shoot consensus map (UNR) showed 258 spots in common and an additional 596 peptides were detected only in the buds. Metabolism, energy, and protein fate were the major functional categories of the common shoot/bud proteins. Proteomic data has been uploaded into PRIDE. ABA metabolism was altered in response to photoperiod treatments; ABA and ABA-GE concentrations were higher under SD and LD, respectively, and are in agreement with transcriptomics data (manuscript in preparation). PARTICIPANTS: This project involves participants from the University of Nevada, Reno, South Dakota State University and Iowa State University. This project is mature and in the writing stage so no additional training has taken place. TARGET AUDIENCES: Information from this project has been presented at national meetings for grape research, the Plant and Animal Genome meeting, and the National Science Foundation. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The data collection and analysis of this type of project takes quite a bit of time, so the impact is delayed until after the project is usually completed. At this point there is little impact, but it is starting with a series of publications this year with more to follow next year. The research is providing a deeper understanding of what molecular processes are changing and controlling bud dormancy in Vitis species. The long-term impact will be to use this information to genetically manage these traits from improve cold tolerance of grapes.
Publications
- 1) Schlauch, K.A., et al. 2010. Transcriptomics analysis methods: microarray data analysis and visualization using the Affymetrix GeneChip Vitis vinifera genome array. In: Methods in Grapevine Research. Or & Delrot, eds. Springer (in press) 2) Lund, S.T. and G.R. Cramer. 2010. Functional genomics: proteomics and metabolomics. In: Grapevine Genomics. Martinez-Zapater & Adam-Blondon, eds. Series: Encyclopedia of Plant Genomics, C. Kole, Series Ed., Science Publishers, Inc. (in press) 3) J. Grimplet, J. Dickerson, A-F. Adam-Blondon, and G.R. Cramer. 2010. Bioinformatics tools in grapevine genomics. In: Grapevine Genomics. Martinez-Zapater & Adam-Blondon, eds. Series: Encyclopedia of Plant Genomics, C. Kole, Series Ed., Science Publishers, Inc. (in press) 4) Zhou, W, and J.A. Dickerson. 2010. Protein Subcellular Localization Prediction based on Structural Features Using Multi-class Support Vector Machine. International Journal of Bioinformatics Research and Applications (submitted). 5) Sreekantan, L., K. Mathiason, J. Grimplet, K. Schlauch, J.A. Dickerson and A. Fennell. 2010. Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning. Plant Molecular Biology (submitted)
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Protein identification is complete and the proteomic data has been uploaded into PRIDE. ABA analyses are completed. PARTICIPANTS: Laurent Deluc (UNR), Kitty Spreeman (UNR), Gouthu Narayanan (UNR), Anne Fennell (SDSU, Julie Dickerson (ISU) and Karen Schlauch (UNR). TARGET AUDIENCES: The grape scientific community. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Proteomic analysis revealed 868 spots in common between Vitis genotypes. Comparison between this bud consensus map and a shoot consensus map (UNR) showed 258 spots in common and an additional 596 peptides were detected only in the buds. Metabolism, energy, and protein fate were the major functional categories of the common shoot/bud proteins. Proteomic data has been uploaded into PRIDE. ABA metabolism was altered in response to photoperiod treatments; ABA and ABA-GE concentrations were higher under SD and LD, respectively, and are in agreement with transcriptomics data (manuscript in preparation).
Publications
- No publications reported this period
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Proteomic and metabolomic assays have been conducted of 5 replicates of treated buds with long-days or short days. PARTICIPANTS: Laurent Deluc (postdoc) and Kitty Spreeman (technician) have worked on this project by grinding samples, extracting protein and metabolites, and running these samples to develop protein and metabolite profiles for both long day and short day treatments over time. One manuscript on the proteomic work is in progress. The metabolite data collection is still in progress. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Data collected are under analysis. There are no conclusions or outputs yet.
Publications
- No publications reported this period
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: Only an annual report to NSF has been disseminated.
PARTICIPANTS: Kitty Spreeman (technician) Laurent Deluc (post-doctoral researcher) Senny Wong (student)
Impacts
Results are incomplete at this time and the data that is collected is under analysis.
Publications
- No publications reported this period
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Progress 01/01/06 to 12/31/06
Outputs
Protocols for protein extraction and metabolite extraction are in the testing phase.
Impacts
Work from this project should lead to a better understanding of the control of bud dormancy and ultimately to improved grape varieties that can produce in more extreme environments.
Publications
- No publications reported this period
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