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

Abstract

BackgroundIn 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.ResultsPyrosequencing 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.ConclusionsThe 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.

The shifting phenological landscape: Within‐ and between‐species variation in leaf emergence in a mixed‐deciduous woodland

“…Spring phenology have been shown to be heritable in a range of species (Frewen et al., 2000; Scotti‐Saintagne et al., 2004), and common garden experiments suggest strong local adaptation (Chmura, 2006; Chmura & Rozkowski, 2002; Hannerz et al., 2003; Jensen & Hansen, 2008). Studies are beginning to identify candidate genes for spring bud development (Alberto et al., 2013; Derory et al., 2006; Morin et al., 2010; Scotti‐Saintagne et al., 2004; Ueno et al., 2013; Zohner & Renner, 2014); knowledge of genes that influence phenological traits will be essential for understanding the mechanisms underlying inherent individual differences in this trait, and the genetic structure of populations.…”

Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting

“…Specifically, this protein is associated with the regulation of plant height as well as leaf size, the latter of which contains young elongation tissues. The relation of CIGR to the regulation of leaf size may indicate the relevance of this protein in the last stages of the bud sprouting development where the leaf is starting to grow [53].…”

“…The agglutinin is considered a glycoprotein and is involved in the immobilization of non-pathogenic bacteria in the different plant tissues [71]. It was previously identified in a white oak study [53], where two stages of bud dormancy were compared. Since, in this work, the dormant bud is represented in the early stages, the over-expression of the gene codifying this protein is consistent with the results determined previously.…”

Interspecific gene flow and maintenance of species integrity in oaks

“…drought tolerance related genes) and reproductive isolation between species (e.g. phenology genes) (Durand et al 2010, Ueno et al 2013. Gene-based EST-SSRs show high transferability between different oak sections (Sullivan et al 2013) and can be used for comparative outlier screens in different oak species to identify gene families related to adaptive species differences.…”