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Genomic-based epidemiology reveals gene flow and independent origins of glyphosate resistance in Bassia scoparia populations across North America
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  • Karl Ravet,
  • Crystal Sparks,
  • Andrea Dixon,
  • Anita Küpper,
  • Eric Westra,
  • Dean Pettinga,
  • Patrick Tranel,
  • Joel Felix,
  • Don Morishita,
  • Prashant Jha,
  • Andrew Kniss,
  • Phillip Stahlman,
  • Paul Neve,
  • Eric Patterson,
  • Philip Westra,
  • Todd Gaines
Karl Ravet
Colorado State University
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Crystal Sparks
Colorado State University
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Andrea Dixon
Rothamsted Research
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Anita Küpper
Bayer CropScience AG
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Eric Westra
Colorado State University
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Dean Pettinga
Colorado State University
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Patrick Tranel
University of Illinois at Urbana-Champaign
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Joel Felix
Oregon State University
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Don Morishita
University of Idaho
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Prashant Jha
Iowa State University
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Andrew Kniss
University of Wyoming
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Phillip Stahlman
Kansas State University
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Paul Neve
Rothamsted Research
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Eric Patterson
Michigan State University
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Philip Westra
Colorado State University
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Todd Gaines
Colorado State University
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Abstract

Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the various units of the EPSPS tandem duplication to investigate whether all glyphosate-resistant plants had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We identified three distinct EPSPS-duplication haplotypes that had geographic associations with the Central Great Plains, Northern Plains, and Pacific Northwest. Population structure revealed a group of populations around the first reported occurrence of glyphosate resistance in the Central Great Plains, a separate group of Pacific Northwest populations, and some relatedness of populations from geographically isolated areas. The results support at least three independent origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.

Peer review status:IN REVISION

30 Oct 2020Submitted to Molecular Ecology
01 Nov 2020Submission Checks Completed
01 Nov 2020Assigned to Editor
12 Nov 2020Reviewer(s) Assigned
25 Jan 2021Review(s) Completed, Editorial Evaluation Pending
01 Mar 2021Editorial Decision: Revise Minor
09 Jul 2021Review(s) Completed, Editorial Evaluation Pending
09 Jul 20211st Revision Received
29 Jul 2021Editorial Decision: Revise Minor
26 Aug 2021Review(s) Completed, Editorial Evaluation Pending
26 Aug 20212nd Revision Received