E-GEOD-32551 - Stage-specific transcriptional changes during zygotic embryogenesis in maritime pine (Pinus pinaster Ait.)

Status
Released on 30 January 2012, last updated on 4 May 2014
Organism
Pinus pinaster
Samples (60)
Array (1)
Protocols (7)
Description
The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified. Pine immature zygotic embryos were pooled into five different developmental groups according to the collection date (Day0; Day5; Day11; Day15 and Day25). A common reference design was used. Total RNA was extracted from each sample. Three extractions were prepared per sample (biological replicates). A defined ammount from each RNA sample was pooled to use as reference. Messenger RNA was amplified for both test samples and reference. These were hybridized together in two separate experiments (technical replicates). In total, 30 slides were analyzed.
Experiment type
transcription profiling by array 
Contacts
Marta Simões <martas@itqb.unl.pt>, Célia Miguel, Jeffrey F Dean, João Maroco, Marta Simões, Rob Alba, W W Lorenz
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-32551.idf.txt
Sample and data relationshipE-GEOD-32551.sdrf.txt
Raw data (1)E-GEOD-32551.raw.1.zip
Processed data (1)E-GEOD-32551.processed.1.zip
Array designA-GEOD-11184.adf.txt
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