title: Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing.
abstract: BACKGROUND
  In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology.
  
  
  RESULTS
  Pyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with both R statistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers ≥ 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR.
  
  
  CONCLUSIONS
  The identification and functional annotation of differentially expressed genes involved in the "response to abscisic acid", "response to cold stress" and "response to oxidative stress" categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.
authors.affiliation: Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki 305-8687 Japan.
authors.forename: Saneyoshi
authors.initials: S
authors.lastname: Ueno
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: Jean Charles
authors.initials: JC
authors.lastname: Leplé
authors.forename: Jérémy
authors.initials: J
authors.lastname: Derory
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Valérie
authors.initials: V
authors.lastname: Léger
authors.forename: Elodie
authors.initials: E
authors.lastname: Prince
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
mesh_terms: D000040:Abscisic Acid / Q000502:physiology; D001483:Base Sequence; D003080:Cold Temperature; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D005875:Gibberellins / Q000235:genetics; D005916:Globulins / Q000235:genetics; D016695:Glycosyltransferases / Q000235:genetics; D018521:Plant Physiological Phenomena / Q000502:physiology*; D029963:Quercus / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D005875:Gibberellins; D005916:Globulins; D018749:RNA, Plant; D000040:Abscisic Acid; D016695:Glycosyltransferases; C473049:xyloglucan - xyloglucosyltransferase