title: Abscisic acid transcriptomic signaling varies with grapevine organ.
abstract: BACKGROUND
  Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns.
  
  
  RESULTS
  Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA.
  
  
  CONCLUSIONS
  This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
authors.forename: Supakan
authors.initials: S
authors.lastname: Rattanakon
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Ghan
authors.affiliation: Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin (ISVV), EGFV, UMR 1287, F-33140, Villenave d'Ornon, France.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Gambetta
authors.affiliation: Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA.
authors.forename: Laurent G
authors.initials: LG
authors.lastname: Deluc
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
authors.forename: Karen A
authors.initials: KA
authors.lastname: Schlauch
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA. cramer@unr.edu.
authors.forename: Grant R
authors.initials: GR
authors.lastname: Cramer
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome; D027843:Vitis / Q000235:genetics / Q000378:metabolism*
chemical_list: D000040:Abscisic Acid
keywords: Abscisic acid signaling; Organ-specificity; Transcriptomics; Vitis vinifera L