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

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Repeated herbicide applications in agricultural fields exert strong selection on weeds such as blackgrass (Alopecurus myosuroides), which is a major threat for temperate climate cereal crops. This inadvertent selection pressure provides an opportunity for investigating 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 target-site resistance (TSR) relies on de novo mutations vs. standing variation is important for developing strategies to manage herbicide resistance. We first 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. Next, through empirical data in the form of highly accurate long-read amplicons of alleles encoding acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS) variants, we showed that most populations with resistance due to TSR mutations-23 out of 27 and six out of nine populations for ACCase and ALS, respectively-contained at least two TSR haplotypes, indicating that soft sweeps are the norm. Finally, through forward-in-time simulations, we inferred that TSR is likely to mainly result from standing genetic variation, with only a minor role for de novo mutations.

Original languageEnglish (US)
Article numbere2206808120
JournalProceedings of the National Academy of Sciences of the United States of America
Volume120
Issue number16
DOIs
StatePublished - Apr 18 2023

All Science Journal Classification (ASJC) codes

  • General

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