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Series GSE23519 Query DataSets for GSE23519
Status Public on Dec 01, 2010
Title Molecular events of apical bud formation in white spruce
Organism Picea glauca
Experiment type Expression profiling by array
Summary 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.
 
Overall design 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.
 
Contributor(s) El Kayal W, Allen CC, Ju CJ, Adams E, King-Jones S, Abrams S, Cooke JE
Citation(s) 21118421
Submission date Aug 09, 2010
Last update date Mar 22, 2012
Contact name Chelsea Ju
E-mail chelsea.ju@ualberta.net
Organization name University of Alberta
Department Biological Sciences
Lab Dr. Janice Cooke
Street address CW 405, Biological Sciences Centre
City Edmonton
State/province Alberta
ZIP/Postal code T6G 2E9
Country Canada
 
Platforms (1)
GPL10754 Arborea spruce 11K cDNA microarray
Samples (26)
GSM604005 SD Day 1 vs. SD Day 0
GSM604006 SD Day 3 vs. SD Day 0
GSM604007 SD Day 7 vs. SD Day 0
Relations
BioProject PRJNA131767

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Supplementary file Size Download File type/resource
GSE23519_RAW.tar 308.0 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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