Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

  1. Anne Plessis
  2. Christoph Hafemeister
  3. Olivia Wilkins
  4. Zennia Jean Gonzaga
  5. Rachel Sarah Meyer
  6. Inês Pires
  7. Christian Müller
  8. Endang M Septiningsih
  9. Richard Bonneau
  10. Michael Purugganan  Is a corresponding author
  1. Plymouth University, United Kingdom
  2. New York University, United States
  3. International Rice Research Institute, Philippines
  4. Simons Foundation, New York, United States
  5. Texas A&M University, United States

Abstract

Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the correspondence of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field.

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Author details

  1. Anne Plessis

    School of Biological Sciences, Plymouth University, Plymouth, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Christoph Hafemeister

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Olivia Wilkins

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Zennia Jean Gonzaga

    International Rice Research Institute, Metro Manila, Philippines
    Competing interests
    The authors declare that no competing interests exist.
  5. Rachel Sarah Meyer

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Inês Pires

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Christian Müller

    Simons Center for Data Analysis, Simons Foundation, New York, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Endang M Septiningsih

    Department of Soil and Crop Sciences, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Richard Bonneau

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Michael Purugganan

    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
    For correspondence
    mp132@nyu.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Plessis et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Anne Plessis
  2. Christoph Hafemeister
  3. Olivia Wilkins
  4. Zennia Jean Gonzaga
  5. Rachel Sarah Meyer
  6. Inês Pires
  7. Christian Müller
  8. Endang M Septiningsih
  9. Richard Bonneau
  10. Michael Purugganan
(2015)
Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions
eLife 4:e08411.
https://doi.org/10.7554/eLife.08411

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https://doi.org/10.7554/eLife.08411