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Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

View ORCID ProfileSonja Kersten, Jiyang Chang, Christian D. Huber, View ORCID ProfileYoav Voichek, Christa Lanz, Timo Hagmaier, View ORCID ProfilePatricia Lang, View ORCID ProfileUlrich Lutz, Insa Hirschberg, Jens Lerchl, Aimone Porri, View ORCID ProfileYves Van de Peer, View ORCID ProfileKarl Schmid, View ORCID ProfileDetlef Weigel, View ORCID ProfileFernando A. Rabanal
doi: https://doi.org/10.1101/2021.12.14.472587
Sonja Kersten
1Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Jiyang Chang
3Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
4Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Christian D. Huber
5Department of Biology, The Eberly College of Science, Penn State University, State College, PA 16801, USA
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Yoav Voichek
6Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Austria
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Christa Lanz
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Timo Hagmaier
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Patricia Lang
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
9Department of Biology, Stanford University, Stanford, CA, USA
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Ulrich Lutz
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Insa Hirschberg
7Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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Jens Lerchl
8BASF SE, Agricultural Research Station, Limburgerhof, Germany
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Aimone Porri
8BASF SE, Agricultural Research Station, Limburgerhof, Germany
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Yves Van de Peer
3Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
4Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
10Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
11College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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Karl Schmid
1Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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Detlef Weigel
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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  • For correspondence: weigel@weigelworld.org
Fernando A. Rabanal
2Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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  • ORCID record for Fernando A. Rabanal
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Abstract

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

Competing Interest Statement

J.L. and A.P. are employees of BASF, which manufactures and sells herbicides. D.W. holds equity in Computomics, which advises breeders. All other authors declare no competing or financial interests.

Footnotes

  • https://keeper.mpdl.mpg.de/d/520501d08acc4bd887f7

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 16, 2021.
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Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Sonja Kersten, Jiyang Chang, Christian D. Huber, Yoav Voichek, Christa Lanz, Timo Hagmaier, Patricia Lang, Ulrich Lutz, Insa Hirschberg, Jens Lerchl, Aimone Porri, Yves Van de Peer, Karl Schmid, Detlef Weigel, Fernando A. Rabanal
bioRxiv 2021.12.14.472587; doi: https://doi.org/10.1101/2021.12.14.472587
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Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Sonja Kersten, Jiyang Chang, Christian D. Huber, Yoav Voichek, Christa Lanz, Timo Hagmaier, Patricia Lang, Ulrich Lutz, Insa Hirschberg, Jens Lerchl, Aimone Porri, Yves Van de Peer, Karl Schmid, Detlef Weigel, Fernando A. Rabanal
bioRxiv 2021.12.14.472587; doi: https://doi.org/10.1101/2021.12.14.472587

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