Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

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.

Deep haplotype analyses of target-site resistance locusACCasein blackgrass enabled by pool-based amplicon sequencing

“…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 ., 2021). 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).…”

“…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 ., 2021). We also find a significant proportion of NTSR for the ACCase inhibiting herbicide Axial® in this German dataset, as the biotests reveal significantly more resistance than the TSR frequencies can explain (Figure S1b,d).…”

“…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 ., 2021). 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.…”

“…For benchmarking purposes, we selected nine populations from our previous study (Kersten et al ., 2021) and compared the ACCase haplotypes determined from 22-24 independently-sequenced individuals to ACCase haplotypes inferred from pools of 200 individuals. Each population was sown separately in the greenhouse.…”

“…For each PCR, we use 50 ng of DNA as a template. The number of template copies in 50 ng of input DNA of a genome estimated to be 3.6 Gbp (Kersten et al, 2021)…”