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Series GSE6027 Query DataSets for GSE6027
Status Public on Oct 14, 2006
Title Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat
Organism Triticum aestivum
Experiment type Expression profiling by array
Summary Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.
Keywords: Time course
 
Overall design The seven stages collected were pre-meiosis (PM), leptotene to pachytene (LP), diplotene to anaphase I (DA), telophase I to telophase II (TT), tetrads (T), immature pollen (IP) and mature anthers (MAN). Immediately after determining the stage, the remaining two anthers from the floret were placed into liquid nitrogen. After collecting at least 25 staged anthers for each time point from several biological samples, anthers from the respective stages were pooled. Leaf material used in this study was collected from glasshouse-grown plants (six weeks) and total RNA isolated using Trizol® (Gibco BRL, Australia) according to the manufacturer’s protocol.
Twenty micrograms of aRNA of from each of the seven samples were fragmented for hybridization to each microarray. In total three technical replicates were conducted for each of the seven stages examined. Affymetrix GeneChip® Wheat Genome Arrays were used for all samples. The arrays were hybridized and processed according to the manufacturer’s specifications.
Normalization of the microarray data was conducted using RMA. The software package Acuity 4 (Molecular Devices, CA, USA) was then used to analyze the microarray data.
 
Contributor(s) Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA
Citation(s) 17052357
Submission date Oct 13, 2006
Last update date Dec 04, 2018
Contact name Jason Alan Able
E-mail(s) jason.able@adelaide.edu.au
Organization name The University of Adelaide
Department School of Agriculture, Food & Wine
Street address Waite Main Building
City Adelaide
State/province SA
ZIP/Postal code 5064
Country Australia
 
Platforms (1)
GPL3802 [wheat] Affymetrix Wheat Genome Array
Samples (21)
GSM139912 Anther pre-meiosis rep1
GSM139914 Anther pre-meiosis rep2
GSM139915 Anther pre-meiosis rep3
Relations
BioProject PRJNA97839

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE6027_RAW.tar 174.0 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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