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Open Access Highly Accessed Research article

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

Saneyoshi Ueno123, Christophe Klopp4, Jean Charles Leplé5, Jérémy Derory23, Céline Noirot4, Valérie Léger23, Elodie Prince23, Antoine Kremer23, Christophe Plomion23 and Grégoire Le Provost23*

Author Affiliations

1 Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki 305-8687 Japan

2 INRA, UMR 1202 BIOGECO, F-33610 Cestas, France

3 Univ. Bordeaux, BIOGECO, UMR 1202, F-33400 Talence, France

4 Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan 31326 France

5 INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans F-45075 France

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BMC Genomics 2013, 14:236  doi:10.1186/1471-2164-14-236

Published: 10 April 2013

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.