Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function
- Colorado State University, United States
- HudsonAlpha Institute for Biotechnology, United States
Abstract
Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses 7 times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files.
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Vegetative Health IndexNational Oceanic and Atmospheric Administration, VHI.
Article and author information
Author details
Funding
National Science Foundation (1022196)
- John K McKay
National Science Foundation (1556262)
- John K McKay
National Science Foundation (1701918)
- John Grey Monroe
U.S. Department of Agriculture (2014- 38420-21801)
- John Grey Monroe
Cargill (Research support)
- John K McKay
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Daniel J Kliebenstein, University of California, Davis, United States
Version history
- Received: August 12, 2018
- Accepted: December 6, 2018
- Accepted Manuscript published: December 6, 2018 (version 1)
- Version of Record published: January 9, 2019 (version 2)
Copyright
© 2018, Monroe 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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Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function
eLife 7:e41038.
https://doi.org/10.7554/eLife.41038
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