E-GEOD-5712 - Transcription profiling by array of Arabidopsis mutant for ADD3

Status
Released on 14 June 2008, last updated on 18 January 2012
Organism
Arabidopsis thaliana
Samples (4)
Array (1)
Protocols (2)
Description
Aims: Comparison of transcriptome between mutant and wild-type plant. Based on the temperature sensitive period of the mutant the gene likely acts during the earliest stages of the specification of the leaf primordium. Background: The ARRESTED DEVELOPMENT 3 mutation causes a temperature dependent loss of all spongy mesophyll and most palisade parenchyma in developing leaves. Although these leaves lack most internal tissues excepting vasculature they continue to expand away from the main axis of plant growth. Mature leaves have a small midrib and marginal regions that are large balloons of epidermis covering airspace. add3 is a temperature sensitive mutation whose most severe phenotypic response occurs at a restrictive temperature of 29 degrees C. Using BAC and TAC filters a recombinant population we have generated and available and newly developed molecular markers a high resolution (1000 chromosomes scored) physical genetic map has been completed to define the physical extent of the locus. Transformation rescue and RNAi experiments are currently underway to determine if a candidate gene identified using the approach outlined above is ADD3. Experimentalia: Wild-type and add3 tissue will be grown at 29 degrees C until the first two true leaves have emerged. Two days after emergence the aerial portions of the plants will be collected and RNA will be isolated. This developmental stage will provide plants with primordia in various stages of development. The wild-type tissue will serve as a control for exposure of developing primordia to high temperature the add3 plants will provide the experimental transcriptome. We intend to use RNA isolation protocols provided by the former AFGC facility for isolation of RNA. Conclusion:ADD3 is the first mutant from our collection of temperature sensitive mutations affecting shoot, floral and root organogenesis to be studied at the transcriptome level. Our work modeling the evolution of gene duplicates and genetic redundancy suggests that temperature conditional redundancy may be common in plants (Pickett and Meeks-Wagner Plant Cell 19957 1347-1356)(Force,Lynch,Pickett et al. Genetics 1999151 1531-1545). A highly similar gene to the ADD3 candidate gene has been identified. An exploration of the utility of transcriptomics to describe phenotypic impacts of potential conditionally redundant mutants is particularly timely. Many reverse genetics experiments in Arabidopsis result in "mutants" displaying small or no impacts on phenotype. The completion of the Arabidopsis genome sequence suggests that this experience may become common. Experimenter name = F. Bryan Pickett; Experimenter institute = Loyola University of Chicago; Experimenter address = Dept. of Biology; Experimenter address = Loyola University of Chicago; Experimenter address = 6525 N. Sheridan Rd. Experimenter address = Chicago, IL; Experimenter zip/postal_code = 60626; Experimenter country = USA Experiment Overall Design: 4 samples were used in this experiment
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-5712.idf.txt
Sample and data relationshipE-GEOD-5712.sdrf.txt
Raw data (1)E-GEOD-5712.raw.1.zip
Processed data (1)E-GEOD-5712.processed.1.zip
Array designA-AFFY-2.adf.txt
R ExpressionSetE-GEOD-5712.eSet.r
Links