Molecular events of apical bud formation in white spruce
Ontology highlight
ABSTRACT:
ORGANISM(S): Picea glauca
PROVIDER: GSE23519 | GEO | 2010/12/01
SECONDARY ACCESSION(S): PRJNA131767
REPOSITORIES: GEO
Similar Datasets
Project description:Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce (Picea glauca [Moench] Voss.), a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for ABA, cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce. Shoot tips (terminal buds), needles, and secondary stems were collected from two-year-old white spruce plants over a 10-week time course of 0, 1, 3, 7, 14, 28, and 70 days after switching from 6 to 8 weeks of long daylight photoperiods (LD; 16 hours of light and 8 hours of dark) to short daylight photoperiods (SD; 8 hours of daylight and 16 hours of dark). Remaining plants were kept in short days for an additional 8-15 weeks, and then transferred to low temperature (LT; 2°C to 4°C) for 3 to 4 weeks with continuing SD prior to harvest. Another set of plants was grown and harvested under the same conditions as described above, but remained in LD at all times. Four sets of dye-swap design microarray experiments were conducted. The first set of experiments (samples 1-7) studied the SD time course of buds development. Terminal buds from each time point (1d, 3d, 7d, 14d, 28d, and 70d) and LT were co-hybridized with actively growing shoot tips (0d). The same time point comparison (without LT) of shoot tips from LD-treated trees was carried out as the second set of experiments (samples 8-13). The third experiment (samples 14-20) denoted a separate LD/SD comparison at seven different time points (0d, 1d, 3d, 7d, 14d, 28d, and 70d), and the last experiment (samples 21-26) compared SD shoot tips, needles, and secondary stems with each of the other tissues at 14d and 70d. In each experiment, four biological replicates were used, with two replicates representing the dye-swaps.
2010-12-01 | E-GEOD-23519 | biostudies-arrayexpress
Project description:In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca [Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development, and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree’s overwintering preparations. For example, genes associated with carbon-based defenses such as terpenoids were downregulated, while many genes associated with proteinbased defenses and other stress mitigation mechanisms were upregulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree’s adaptive response to overwintering. Two year old white spruce (Picea glauca [Moench] Voss) seedlings were used for all experiments, which were conducted as described by El Kayal et al. (2011). Using a complete randomized block design, seedlings were grown in growth chambers under long days (LD; 16h day / 8h night, 20°C, 50 to 60% RH) for 8-10 weeks. Shortly before seedlings were to begin bud formation, the photoperiod was changed to short days (SD; 8h day / 16h night, 20°C, 50 to 60% RH) to induce rapid and synchronous bud formation. This was designated Day 0. Lignified whole stems representing the current year’s growth (microarrays, microscopy) or previous year’s growth (protein analyses) were sampled at 0, 3, 7, 14, 28 and 70 d (10 wk) SD, and immediately frozen in liquid nitrogen. Remaining plants were maintained in SD for an additional 8-15 wk, and then transferred to low temperatures (LT, 2 - 4°C) for 3 to 4 weeks with continuing SD prior to harvest. These are referred to as LT samples.
2011-10-16 | E-GEOD-31090 | biostudies-arrayexpress
Project description:It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions. While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20°C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce.
2014-09-01 | GSE57172 | GEO
Project description:It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions. While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20M-BM-0C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce. A clonally replicated QTL mapping population (cross C94-1-2516, M-bM-^YM-^@77111 M-CM-^W M-bM-^YM-^B2388), previously characterized by Pelgas et al. (2011), was used for this study. Phenotypic data collected between 2006-2008 was used to identify extremes for time to bud set within the QTL population. Genotypes falling within the lower quartile for time to bud set for at least three of six experiments were designated as early time to bud set, while genotypes falling within the upper quartile for time to bud set for at least three of six experiments were designated as late time to bud set. Shoot tips from four ramets of each genotype were harvested for molecular analysis. Two ramets were harvested at the first sign of bud formation (Time 1) and the remaining two ramets were harvested six weeks later at which time the majority of seedlings were at the mid stage of bud set (Time 2). Microarray hybridizations were conducted to make the following comparisons: a comparison of bud development (Time 1 v. Time 2) in early time to bud set seedlings, a comparison of bud development (Time 1 v. Time 2) in late time to bud set seedlings, and a comparison of early and late time to bud set seedlings within early stages of bud formation or mid stage of bud formation. Each of two biological replicates for each time point and each phenotypic class was hybridized.
2014-09-01 | E-GEOD-57172 | biostudies-arrayexpress
Project description:Molecular events of apical bud formation in white spruce
| PRJNA131767 | ENA
Project description:We report the discovery of a beta-glucosidase gene (Pgβglu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. Pgβglu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in Pgβglu-1 expression may be a key for the adaptability of spruce populations.
2014-05-06 | GSE57301 | GEO
Project description:The goal of this study was to generate a spatiotemporal atlas of gene expression in the developing salivary gland. This will allow us to identify changes in gene expression that may result in the formation of the different domains of the salivary gland. At least 4 microarrays per location per time point were collected. The originating samples are rather small, so many clefts, ducts and buds had to be pooled to generate enough aRNA for hybridization. Supplementary file: cluster heat map from anova 0.05 passing entities, E12.5 main bud vs E15 main bud (averaged readings)
2011-07-01 | E-GEOD-22828 | biostudies-arrayexpress
Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants. Examination of small RNA populations in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.)
2012-12-31 | E-GEOD-38894 | biostudies-arrayexpress
Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants.
2012-12-31 | GSE38894 | GEO
Project description:We report the discovery of a beta-glucosidase gene (PgM-NM-2glu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. PgM-NM-2glu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in PgM-NM-2glu-1 expression may be a key for the adaptability of spruce populations. Transcriptome profiling was carried out with needles from 7 resistant and 7 non-resistant trees (harvested on June 17th, 2010), and 3 samples per tree (n=42) with a custom microarray developed for spruce species and comprising oligonucleotide probes for 23,853 unique P. glauca gene sequences (Raherison et al., 2012).
2014-05-06 | E-GEOD-57301 | biostudies-arrayexpress