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Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierForestry and Forest Products Research Institute [FFPRI]
dc.contributor.authorUENO, Saneyoshi
hal.structure.identifierUnité de Mathématiques et Informatique Appliquées de Toulouse [MIAT INRA]
dc.contributor.authorKLOPP, Christophe
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorLEPLÉ, Jean-Charles
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDERORY, Jérémy
hal.structure.identifierUnité de Mathématiques et Informatique Appliquées de Toulouse [MIAT INRA]
dc.contributor.authorNOIROT, Céline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Valérie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPRINCE, Elodie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
dc.date.issued2013
dc.identifier.issn1471-2164
dc.description.abstractEnBackground 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.
dc.language.isoen
dc.publisherBioMed Central
dc.title.enTranscriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-14-236
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halMathématiques [math]
dc.subject.halInformatique [cs]
bordeaux.journalBMC Genomics
bordeaux.page15 p.
bordeaux.volume14
bordeaux.peerReviewedoui
hal.identifierhal-02650124
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02650124v1
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