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In silico search for drought-responsive genes in plants on the basis of scientific data: case study on poplar roots

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Abstract

Despite of a number of studies on the genetic nature of plant adaptation to drought stress there is still no conclusion on the core mechanism of defense. Extraction of knowledge gained from experiments on different plant species under different conditions and subsequent interpolation thus appears to be a challenge. Here we applied a sequence similarity-based approach to identify computationally the components of defense against water deprivation. The prediction in silico was based on the available scientific data. We identified a subset of defense gene candidates, of which 2 % were experimentally proven to be drought-responsive. The transcriptomic analysis of drought-stressed poplar roots generated data that confirm and/or complement previous reports on plant responses to drought. On the other hand, we observed suppression of genes involved in antioxidative defense that seems to contradict many foregoing observations. The results, advantages and possible drawbacks of our prediction approach are discussed in light of experimental data.

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Acknowledgments

Research on this paper was facilitated by a Hertha Firnberg Grant for I.M. from the Austrian National Science Fund.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str. 24, 3430, Tulln, Austria

    Dieter Kopecky, Astrid Heide Sziderics, Friederike Trognitz, Nadine Spieß, Michael Stierschneider & Silvia Fluch

  2. Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, P.O. Box 39A, 95007, Nitra, Slovak Republic

    Ildikó Matušíková

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  1. Dieter Kopecky
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  2. Ildikó Matušíková
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  3. Astrid Heide Sziderics
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  4. Friederike Trognitz
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  5. Nadine Spieß
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  6. Michael Stierschneider
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  7. Silvia Fluch
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Correspondence to Ildikó Matušíková.

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Communicated by M. Stobiecki.

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Kopecky, D., Matušíková, I., Sziderics, A.H. et al. In silico search for drought-responsive genes in plants on the basis of scientific data: case study on poplar roots. Acta Physiol Plant 35, 1955–1966 (2013). https://doi.org/10.1007/s11738-013-1234-9

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  • DOI: https://doi.org/10.1007/s11738-013-1234-9

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