Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

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.

Deep haplotype analyses of target‐site resistance locus ACCase in blackgrass enabled by pool‐based amplicon sequencing

“…In a recent study, we sequenced PacBio long‐read amplicons of the TSR locus ACCase in individuals of 47 European A. myosuroides populations (Kersten et al ., 2023). We discovered a recurrent pattern within field populations of different haplotypes with the same TSR mutation resulting from independent mutation events, as opposed to the same TSR mutation being transferred to other haplotypes by recombination.…”

“…If, on the other hand, multiple adaptive haplotypes in a population increase in frequency at the same time, this is called a soft sweep (Hermisson and Pennings, 2017). In 38 of 55 German A. myosuroides populations containing TSR mutations, we can observe the latter phenomenon, confirming our previous results from European populations where herbicide adaptation occurred predominantly via soft sweeps through TSR mutations of independent origin (Kersten et al ., 2023). We also find a significant proportion of NTSR for the ACCase ‐inhibiting herbicide Axial ® in this German data set, as the biotests reveal significantly more resistance than the TSR frequencies can explain (Figure S3a,c).…”

“…Among the nine phenotypically sensitive populations included in the study, there were two organically farmed fields that have not been treated with herbicides going back as far as at least 1980, which predates the introduction of ACCase inhibitors to the market. In these fields, we found TSR haplotypes at low frequencies, from 0.3% to 2.0% (Figure 4), in agreement with our previous inferences that standing genetic variation is the most likely evolutionary mechanism behind herbicide selection (Kersten et al ., 2023). This is considerably higher than in a phenotyping‐based study of the grass Lolium rigidum , the frequency of resistant individuals to ALS inhibitors in untreated populations ranged from 0.001% to 0.012% (Preston and Powles, 2002).…”

“…Within this range, we included the reported selection coefficient estimates for TSR mutations Trp2027Cys and Asp2078Gly, for which under realistic field scenarios, seed production was significantly reduced by 20% and 30%, respectively (Du et al ., 2019). Other parameters, such as effective population size, mutation and recombination rate, were obtained from the literature (Bauer et al ., 2013; Kersten et al ., 2023; Yang et al ., 2017). For each mutation and initial allele frequency, we simulated two different dominance coefficients derived from fitness experiments in A. myosuroides (Menchari et al ., 2008), an intermediate, codominant coefficient of 0.5 (Figure 5a–d), and a recessive coefficient of 0.25 (Figure 5e–h).…”

“…The frequencies of ACCase TSR mutations have been investigated in several studies (Délye et al ., 2010; Délye et al ., 2004b; Menchari et al ., 2006; Rosenhauer et al ., 2013), but usually without considering the genomic context of the complete ACCase gene. Complete haplotype information is important in several respects, including establishing the number of times with which a specific mutation has occurred independently, and whether TSR mutations occur preferentially on specific haplotype backgrounds (Kersten et al ., 2023; Kreiner et al ., 2022).…”