DATA, MATERIALS, AND SOFTWARE AVAILABILITY : Raw data including PacBio CLR
and Iso-seq reads, Illumina PCR-free, Hi-C, and RNA-seq reads can be accessed
in the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena/browser/
home) under project accession number PRJEB49257 (78), assembly accession
CASDCE010000000 (79). Raw ddRAD-seq data for the population study, and
PacBio CCS q20 reads can be downloaded from the ENA project accession number
PRJEB49288 (80). Annotation files for the genome assembly, the SNP matrix
for the ddRAD-seq experiment, and the fasta files with the haplotypes of ACCase
and ALS can be found at https://doi.org/10.5281/zenodo.7634530 (81). Scripts
and experimental protocols to reproduce the analyses in this study are deposited
in the GitHub repository of this study (https://github.com/SonjaKersten/
Herbicide_resistance_evolution_in_blackgrass_2022) (82).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.The Landesgraduiertenförderung (State Graduate Scholarship, LGFG) of the State of Baden-Württemberg; a Human Frontiers Science Program Long-Term Fellowship, BASF and the Max Planck Society.https://www.pnas.org/am2024Biochemistry, Genetics and Microbiology (BGM)SDG-15:Life on lan
