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Status |
Public on Jan 30, 2012 |
Title |
Stage-specific transcriptional changes during zygotic embryogenesis in maritime pine (Pinus pinaster Ait.) |
Platform organism |
Pinus taeda |
Sample organism |
Pinus pinaster |
Experiment type |
Expression profiling by array
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Summary |
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.
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Overall design |
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.
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Contributor(s) |
Simões M, Lorenz WW, Maroco J, Alba R, Dean JF, Miguel C |
Citation(s) |
23987738 |
Submission date |
Oct 03, 2011 |
Last update date |
Apr 24, 2014 |
Contact name |
Marta Simões |
E-mail(s) |
martas@itqb.unl.pt
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Organization name |
IBET
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Lab |
Forest Biotech
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Street address |
Quinta do Marquês - EAN
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City |
Oeiras |
ZIP/Postal code |
2781-901 |
Country |
Portugal |
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Platforms (1) |
GPL11184 |
Loblolly pine 26K cDNA array v2.0, PtGen2 |
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Samples (30)
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GSM806967 |
Collection day 0 biological replicate 1, technical replicate 1 |
GSM806968 |
Collection day 0 biological replicate 1, technical replicate 2 |
GSM806969 |
Collection day 0 biological replicate 2, technical replicate 1 |
GSM806970 |
Collection day 0 biological replicate 2, technical replicate 2 |
GSM806971 |
Collection day 0 biological replicate 3, technical replicate 1 |
GSM806972 |
Collection day 0 biological replicate 3, technical replicate 2 |
GSM806973 |
Collection day 5 biological replicate 1, technical replicate 1 |
GSM806974 |
Collection day 5 biological replicate 1, technical replicate 2 |
GSM806975 |
Collection day 5 biological replicate 2, technical replicate 1 |
GSM806976 |
Collection day 5 biological replicate 2, technical replicate 2 |
GSM806977 |
Collection day 5 biological replicate 3, technical replicate 1 |
GSM806978 |
Collection day 5 biological replicate 3, technical replicate 2 |
GSM806979 |
Collection day 11 biological replicate 1, technical replicate 1 |
GSM806980 |
Collection day 11 biological replicate 1, technical replicate 2 |
GSM806981 |
Collection day 11 biological replicate 2, technical replicate 1 |
GSM806982 |
Collection day 11 biological replicate 2, technical replicate 2 |
GSM806983 |
Collection day 11 biological replicate 3, technical replicate 1 |
GSM806984 |
Collection day 11 biological replicate 3, technical replicate 2 |
GSM806985 |
Collection day 15 biological replicate 1, technical replicate 1 |
GSM806986 |
Collection day 15 biological replicate 1, technical replicate 2 |
GSM806987 |
Collection day 15 biological replicate 2, technical replicate 1 |
GSM806988 |
Collection day 15 biological replicate 2, technical replicate 2 |
GSM806989 |
Collection day 15 biological replicate 3, technical replicate 1 |
GSM806990 |
Collection day 15 biological replicate 3, technical replicate 2 |
GSM806991 |
Collection day 25 biological replicate 1, technical replicate 1 |
GSM806992 |
Collection day 25 biological replicate 1, technical replicate 2 |
GSM806993 |
Collection day 25 biological replicate 2, technical replicate 1 |
GSM806994 |
Collection day 25 biological replicate 2, technical replicate 2 |
GSM806995 |
Collection day 25 biological replicate 3, technical replicate 1 |
GSM806996 |
Collection day 25 biological replicate 3, technical replicate 2 |
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Relations |
BioProject |
PRJNA147015 |
Supplementary file |
Size |
Download |
File type/resource |
GSE32551_RAW.tar |
23.1 Mb |
(http)(custom) |
TAR (of TXT) |
Processed data included within Sample table |
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