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Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants

Rahul Bhosale, Jeremy B. Jewell, Jens Hollunder, Abraham J.K. Koo, Marnik Vuylsteke, Tom Michoel, Pierre Hilson, Alain Goossens, Gregg A. Howe, John Browse, Steven Maere
Rahul Bhosale
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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  • ORCID record for Rahul Bhosale
Jeremy B. Jewell
Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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Jens Hollunder
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Abraham J.K. Koo
Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Marnik Vuylsteke
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Tom Michoel
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Pierre Hilson
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Alain Goossens
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Gregg A. Howe
Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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John Browse
Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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Steven Maere
Department of Plant Systems Biology, VIB, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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  • For correspondence: steven.maere@psb.vib-ugent.be

Published August 2013. DOI: https://doi.org/10.1105/tpc.113.112268

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  • © 2013 American Society of Plant Biologists. All rights reserved.

Abstract

Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.

  • Glossary

    ANOVA
    analysis of variance
    GO
    Gene Ontology
    FDR
    false discovery rate
    JA
    jasmonic acid
    ABA
    abscisic acid
    JA-Ile
    jasmonoyl-Ile
    Col-0
    Columbia-0
    MeJA
    methyl jasmonate
    • Received April 3, 2013.
    • Revised June 16, 2013.
    • Accepted July 18, 2013.
    • Published August 13, 2013.
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    Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants
    Rahul Bhosale, Jeremy B. Jewell, Jens Hollunder, Abraham J.K. Koo, Marnik Vuylsteke, Tom Michoel, Pierre Hilson, Alain Goossens, Gregg A. Howe, John Browse, Steven Maere
    The Plant Cell Aug 2013, 25 (8) 2865-2877; DOI: 10.1105/tpc.113.112268

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    Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants
    Rahul Bhosale, Jeremy B. Jewell, Jens Hollunder, Abraham J.K. Koo, Marnik Vuylsteke, Tom Michoel, Pierre Hilson, Alain Goossens, Gregg A. Howe, John Browse, Steven Maere
    The Plant Cell Aug 2013, 25 (8) 2865-2877; DOI: 10.1105/tpc.113.112268
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    The Plant Cell Online: 25 (8)
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    Aug 2013
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