Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change

  1. Megan Ann Supple  Is a corresponding author
  2. Jason G Bragg
  3. Linda M Broadhurst
  4. Adrienne B Nicotra
  5. Margaret Byrne
  6. Rose L Andrew
  7. Abigail Widdup
  8. Nicola C Aitken
  9. Justin O Borevitz
  1. The Australian National University, Australia
  2. Commonwealth Scientific and Industrial Research Organisation, Australia
  3. Department of Parks and Wildlife Western Australia, Australia
  4. University of New England, Australia

Abstract

As species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions. Eucalyptus melliodora is a foundation species of a critically endangered community in Australia that is a target for restoration. We examined genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining high levels of gene flow extending for 500 km and correlations with climate and soil variables. Growth experiments revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Model predictions suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model to E. melliodora restoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration.

Data availability

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Megan Ann Supple

    Research School of Biology, The Australian National University, Canberra, Australia
    For correspondence
    megan.a.supple@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0204-7852
  2. Jason G Bragg

    Research School of Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  3. Linda M Broadhurst

    Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  4. Adrienne B Nicotra

    Research School of Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  5. Margaret Byrne

    Science and Conservation Division, Department of Parks and Wildlife Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7197-5409
  6. Rose L Andrew

    School of Environmental and Rural Science, University of New England, Armidale, Australia
    Competing interests
    The authors declare that no competing interests exist.
  7. Abigail Widdup

    Research School of Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  8. Nicola C Aitken

    Research School of Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
  9. Justin O Borevitz

    Research School of Biology, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.

Funding

Australian Research Council (Linkage Grant LP130100455)

  • Jason G Bragg
  • Linda M Broadhurst
  • Adrienne B Nicotra
  • Margaret Byrne
  • Justin O Borevitz

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2018, Supple 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.

Metrics

  • 3,547
    views
  • 434
    downloads
  • 59
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Megan Ann Supple
  2. Jason G Bragg
  3. Linda M Broadhurst
  4. Adrienne B Nicotra
  5. Margaret Byrne
  6. Rose L Andrew
  7. Abigail Widdup
  8. Nicola C Aitken
  9. Justin O Borevitz
(2018)
Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change
eLife 7:e31835.
https://doi.org/10.7554/eLife.31835

Share this article

https://doi.org/10.7554/eLife.31835

Further reading

    1. Plant Biology
    2. Structural Biology and Molecular Biophysics
    Théo Le Moigne, Martina Santoni ... Julien Henri
    Research Article

    The Calvin-Benson-Bassham cycle (CBBC) performs carbon fixation in photosynthetic organisms. Among the eleven enzymes that participate in the pathway, sedoheptulose-1,7-bisphosphatase (SBPase) is expressed in photo-autotrophs and catalyzes the hydrolysis of sedoheptulose-1,7-bisphosphate (SBP) to sedoheptulose-7-phosphate (S7P). SBPase, along with nine other enzymes in the CBBC, contributes to the regeneration of ribulose-1,5-bisphosphate, the carbon-fixing co-substrate used by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The metabolic role of SBPase is restricted to the CBBC, and a recent study revealed that the three-dimensional structure of SBPase from the moss Physcomitrium patens was found to be similar to that of fructose-1,6-bisphosphatase (FBPase), an enzyme involved in both CBBC and neoglucogenesis. In this study we report the first structure of an SBPase from a chlorophyte, the model unicellular green microalga Chlamydomonas reinhardtii. By combining experimental and computational structural analyses, we describe the topology, conformations, and quaternary structure of Chlamydomonas reinhardtii SBPase (CrSBPase). We identify active site residues and locate sites of redox- and phospho-post-translational modifications that contribute to enzymatic functions. Finally, we observe that CrSBPase adopts distinct oligomeric states that may dynamically contribute to the control of its activity.

    1. Plant Biology
    Maryam Rahmati Ishka, Hayley Sussman ... Magdalena M Julkowska
    Research Article

    Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.