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White bars, number of samples collected. Black bars, number of samples successfully genotyped at ACCase codon 1781 using dCAPS. N.d., specimen collection year not determined.
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Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic v...
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Citations
... Standing variation for herbicide resistance was present in populations of weeds such as annual ryegrass (Lolium rigidum) and blackgrass (Alopecurus myosuroides) that were never exposed to herbicides, even predating their introduction in blackgrass (Preston and Powles, 2002;Délye, Deulvot, and Chauvel, 2013). Recent genomic analysis and simulations by Kersten et al. (2023) highlight the prevalent role of standing genetic variation in target-site resistance adaptation of the annual weed blackgrass. ...
The recurrent exposure to herbicides in agricultural landscapes forces weeds to adapt in a race against extinction. What role newly arising mutations and pre-existing variation play in this evolution of herbicide resistance is critical for developing management strategies. Here, we present a model of rapid adaptation in response to strong selection, capturing complex life cycles of sexual and asexual reproduction and dormancy in a perennial weed. Using a multitype Galton-Watson process, we derive the probability of herbicide resistance evolution and the waiting time distribution until resistant plants appear in the field. We analyse the effect of seed bank dynamics and details of the reproductive system in defining the probability and timing of resistance adaptation in Sorghum halepense. Further, we investigate key factors determining the primary source of adaptive variation. We find that even small fitness costs associated with resistance reduce adaptation from standing genetic variation. For herbicide resistance inherited in a (incompletely) dominant fashion, self-pollination also diminishes standing variation for herbicide resistance by increasing the homozygosity. Our study highlights the importance of seed banks for weeds' adaptive potential, preserving genetic information of forgone selection and prolonging the period in which the population can adapt.
... By combining their genetic data and metadata, we can measure the habitat ranges of species through time and identify possible associations between such changes and climatic or anthropogenic events. In one example, the genetic analysis of the grass Alopecurus myosuroides from herbarium collections showed that the genetic variants associated with herbicide resistance in this plant pre-dated the use of herbicides, which confirmed that this resistance did not evolve from anthropogenic events (Délye et al. 2013). ...
Over the last few centuries, millions of plant specimens have accumulated within herbaria and biocultural collections. These include type specimens, used to define species, and populations that are rare, extinct or difficult to access. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and become increasingly difficult to characterise their genetic signatures, even considering exponential advancements in sequencing technologies. Here, we tested the genotyping performance on highly degraded samples using a commonly used high-throughput sequencing (HtS) technique, genome skimming, against a recent alternative target capture kit, the universal set Angiosperm-353. We performed phylogenomic analyses of modern leaf and historical barks of Cinchona, including 23 historical barks and six fresh leaf specimens. DNA within historical barks is highly degraded, therefore a customised DNA extraction method was developed before library preparation. We show that sample degradation over time directly impacted the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we find that both approaches generate enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. Within historical barks, the target capture kit is more advantageous than genome skimming in profiling Cinchona species since it was possible to retrieve nuclear and plastid data to infer phylogenies. This study showcases the value of historical samples in genetic studies and paves the way for further experiments across different taxonomic groups with varying levels of genetic variation or hybridisation.
... Devising effective strategies for managing herbicide resistance necessitates determining whether resistance mutations originate de novo or were present in the existing genetic variation and to what extent gene flow plays a role in spreading herbicide resistance. Genotyping herbarium specimens of blackgrass (Alopecurus myosuroides) revealed that an herbicide resistance mutation located in the direct target of herbicides (target-site resistance) was segregating at a very low frequency approximately one century before the introduction of herbicides (30). A recent genomics study using contemporary samples also suggested that standing genetic variation plays a crucial role in facilitating the rapid evolution of target-site herbicide resistance (31). ...
Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.
... Standing genetic variation for herbicide resistance has been found in plant populations never exposed to herbicides, among others, target-site resistance against ACCase-inhibitors 28 . Moreover, herbicide resistance adaptation may primarily proceed from standing genetic variants as the initial frequency of resistant individuals may be much higher than the spontaneous mutation rate of resistance alleles 27,28 . Thus, we also include standing genetic variation in our model and derive an analytic approximation of the expected variation (v) in an untreated field. ...
... 39). In another study one individual carrying a specific ACCase target-site resistance was detected in a sample of 685 blackgrass (Alopecurus myosuroides) specimens collected before the introduction of ACCase-inhibiting herbicides 28 . This abundance corresponds to a resistance allele frequency of 7.3 × 10 −4 . ...
... However, for a fitness cost on seed production of 30%, reported for a mutant ACCase allele endowing herbicide resistance in Johnsongrass 30 , the expected resistance allele frequency and cumulative frequency of resistant types range from 3.3 × 10 −8 to 5.3 ×10 −8 and 4.9 × 10 −8 to 7.3 × 10 −8 , respectively, depending on the dominance of this fitness cost. This initial prevalence of target-site resistance is in the order of the spontaneous mutation rate 37,38 and considerably lower than what is reported in the literature 28,39 . ...
Herbicide-resistant weeds pose a substantial threat to global food security. Perennial weed species are particularly troublesome. Such perennials as Sorghum halepense spread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study of S. halepense incorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data of S. halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation of S. halepense. While self-pollination accelerates target-site resistance evolution, seed banks considerably increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and mono-treatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.
... This is considerably higher than in a phenotypingbased 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). The observation of TSR mutations in organic fields without a history of herbicide use is in agreement with the ACCase TSR mutation Ile1781Leu having been detected in one out of 685 (0.146%, or 0.073% at the haplotype level) A. myosuroides herbarium specimens collected about a 100 years ago (Délye et al., 2013a). Under herbicide selection, strong resistance can develop within a few generations in such populations. ...
Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in only a few generations. Target‐site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long‐read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool‐based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof‐of‐concept study, we sequenced with PacBio High Fidelity (HiFi) reads long‐range amplicons (13.2 kb) encompassing the entire ACCase gene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools in plants and other organisms. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany‐wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward‐in‐time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, highlighting the importance of accurate measurement of TSR haplotype prevalence for weed management.
... The gene(s) that confer resistance to a given herbicide may be present(s) in a population before even this herbicide is released on the market. The greatest evidence of this was found in A. myosuroides from plants of a herbarium from France collected in 1888, in which an individual presented the mutation lIe-1781-Leu in its heterozygous form, widely reported as responsible for conferring resistance to ACCase inhibitors (Délye et al. 2013a, b). However, the presence of this mutation occurred 90 years before this group of herbicides were first developed and used. ...
... Figure 8 shows the route of a herbicide from the moment of application to the death of a sensitive plant, which is an ideal condition of chemical control of weeds. After herbicide application, the molecules penetrate the plant (leaf or root absorption), are translocated to short (contact herbicides) or long distances (systemic herbicides) to the target site, where the herbicide is connected, disrupting biosynthesis pathways or vital cellular structures and/or generating cytotoxic molecules (e.g., reactive oxygen that damages cells), and ultimately cause plant death (Délye et al. 2013a, b). ...
Chemical control is an efficient method and the most used in agriculture; however, resistant weeds have evolved worldwide due to the selection pressure caused by the repeated use of herbicides with the same mechanism of action. Some mechanisms of action have a greater disposition to evolve resistance, with the Acetolactate Synthase (ALS) and Photosystem II (PSII) inhibitors. Resistant biotypes seriously compromise agricultural crops, making management difficult and
increasing control costs; therefore, management alternatives must be adopted to
minimize the damage caused by resistant biotypes. For genetically modified varieties,
such as glyphosate-resistant soybeans, other herbicides with different mechanisms
of action are being included in management programs to control resistant
biotypes. The use of herbicides with different mechanisms of action in annual rotations,
tank mixes and sequential applications, can delay the evolution of resistance,
minimizing the selection pressure imposed by a single specific mechanism of action.
Integrated weed management combining different control methods is a viable alternative for controlling resistant biotypes. Thus, the chapter covers the evolution of resistance in the world and in Brazil, the different mechanisms of resistance to target and non-target site, methods of identification of resistant biotypes, and alternatives
for integrated management of herbicide resistant weeds.
... Quelques études ont commencé à explorer l'implication de la méthylation de l'ADN dans la régulation de l'expression de gènes impliqués dans la détoxication d'herbicides Margaritopoulou et al. 2018 ;Nardemir et al. 2015 ; (Barrett & Schluter 2008). À l'appui de cette dernière hypothèse, des allèles connus pour être directement impliqués dans la résistance ont été détectés dans des populations n'ayant jamais été exposées aux herbicides (Délye, Deulvot, et Chauvel 2013 ;Mengistu, Messersmith, et Christoffers 2003). ...
Common ragweed (Ambrosia artemisiifolia L.), a particularly troublesome and allergenic weed, is mainly controlled in agricultural fields using ALS inhibitor herbicides. Recent cases of herbicide resistance have been reported in France and are jeopardising the efficacy of this mode of action. Both target site resistance (TSR, structural mutation in ALS gene) and non target site resistance (NTSR, regulatory and/or structural mutations in secondary metabolism) are involved. The fundamental aim of this work was to identify the genetic determinisms of resistance to ALS inhibitors that have evolved in common ragweed populations in France. As an applied objective, this work also aimed to prepare the development of a high- throughput molecular diagnostic tool that would ensure a rapid detection of resistance. We first assessed the situation of common ragweed resistance in France and identified the mechanisms involved and their modalities of evolution. Using herbicide sensitivity bioassays coupled with ALS gene sequencing, we showed that ragweed resistance to two active substances, imazamox and tribenuron, is emerging in France and is mainly due to NTSR mechanisms. The observed resistance patterns suggest that a diversity of NTSR mechanisms are evolving in France. Furthermore, we demonstrated that TSR evolved locally, through multiple and independent appearance of mutations in the ALS gene. Thanks to the innovative application of high- throughput sequencing for the diagnosis of TSR on a national scale, we identified several foci of TSR emergence, as well as an unsuspected diversity of mutations in the ALS gene. We then studied the genetic determinisms of NTSR. A transcriptomic approach (RNASeq) associated with an analysis of nucleotide polymorphisms was conducted, based on the hypothesis that genes and/or markers of NTSR differed by their expression level and/or by sequence polymorphisms between plants resistant or sensitive to ALS inhibitors. For the first time, this approach was conducted directly on field plant material, i.e. six populations with distinct geographical origins and/or resistance profiles. Constitutive expression differences between resistant and sensitive plants were identified, especially in genes from families known to be involved in herbicide metabolism (cytochromes P450, transferase enzymes, transporters, etc.), but also in genes that may be involved in regulatory cascades activated by the herbicide. Validation of their relative expression levels and their ability to predict NTSR was performed on a massive sampling of plants. Taken together, the results indicate that a very high diversity of mechanisms is involved in RNLC within and between populations, highlighting the highly polygenic nature of RNLC in ragweed. In addition, assessment of the early response of plants to herbicide application showed that genes involved in secondary plant metabolism are specifically induced by treatment in resistant plants from different populations. Finally, sequence variants potentially correlated with NTSR were identified. Their validity as resistance markers remains to be confirmed. The diversity of resistance mechanisms identified within each population renders the development of a molecular diagnosis tool complex. On the other hand, it opens exciting perspectives for the study of the evolutionary dynamics of the adaptation of an invasive species subjected to a particularly intense anthropogenic selection pressure.
... Similar to the acetyl-CoA carboxylase Ile-1781-Leu resistance point mutation, a fitness advantage associated with the Val-202-Phe would suggest no apparent constraints for the allele to persist and be fixed in L. rigidum and other species, in the absence of herbicide selection. [48][49][50] Therefore, reducing dinitroaniline herbicide selection pressure is unlikely to decrease the population frequency of the Val-202-Phe mutation, and other weed control strategies (alternate chemical, mechanical, biological and cultural) would be required to delay and mitigate resistance evolution associated with this particular mutation. ...
BACKGROUND
Lolium rigidum is the most important weed in Australian agriculture and pre‐emergence dinitroaniline herbicides (e.g., trifluralin) are widely and persistently used for Lolium control. Consequently, evolution of resistance to dinitroaniline herbicides has been increasingly reported. Resistance‐endowing target‐site α‐tubulin gene mutations are identified with varying frequency. This study investigated the putative fitness cost associated with the common resistance mutation Val–202–Phe and the rare resistance mutation Arg–243–Met causing helical plant growth.
RESULTS
Results showed a deleterious effect of Arg–243–Met on fitness when plants are homozygous for this mutation. This was evidenced as high plant mortality, severely diminished root and aboveground vegetative growth (lower relative growth rate), and very poor fecundity compared with the wild‐type, which led to a nearly lethal fitness cost of >99.9% in competition with a wheat crop. A fitness penalty in vegetative growth was evident, but to a much lesser extent, in plants heterozygous for the Arg–243–Met mutation. By contrast, plants possessing the Val–202–Phe mutation exhibited a fitness advantage in vegetative and reproductive growth.
CONCLUSION
The α‐tubulin mutations Arg–243–Met and Val–202–Phe have contrasting effects on fitness. These results help understand the absence of plants homozygous for the Arg–243–Met mutation and the high frequency of plants carrying the Val–202–Phe mutation in dinitroaniline‐resistant L. rigidum populations. The α‐tubulin Arg–243–Met mutation can have an exceptional fitness cost with nearly lethal effects on resistant L. rigidum plants. © 2022 Society of Chemical Industry.
... It is unknown what the relative contributions of each are to herbicide resistance. Standing variation that would confer herbicide resistance was present in Alopecurus myusoroides specimens collected before herbicides were invented (Délye et al. 2013a). Studies investigating the standing variation of herbicide resistance of Lolium rigidum found rates of resistance to AHAS-inhibitors between 2.2 × 10 −5 and 1.2 × 10 −4 (Preston and Powles 2002). ...
Research on maize weeds in New Zealand is extensive, but few systematic efforts were made to catalogue weed species and determine their prevalence and abundance. Broadleaf weeds were early problems but became manageable when photosystem-II inhibitors and synthetic auxins were introduced in the 1950s. Annual grasses became the next problematic weeds, and newer herbicides were introduced in the 1970s. The first cases of resistance were reported in the 1980s, Chenopodium album L. and Persicaria maculosa Gray both evolved resistance atrazine after several years of selection. Perennial weeds Oxalis latifolia and Calystegia sepium ssp. roseata were identified as problem weeds. More herbicides were introduced. Atrazine-resistant C. album evolved additional resistance to dicamba in the eastern Waikato. The quarantine weed Abutilon theophrasti was unintentionally introduced to multiple maize farms. Most recently, the annual grass Digitaria sanguinalis evolved resistance to nicosulfuron in Bay of Plenty and Waikato maize. The most recent ‘weeds survey’ in maize is two decades old, in twenty Waikato, four Bay of Plenty and six Gisborne maize fields. Above-ground (spring seedlings) and below-ground (soil seedbank) weeds were recorded. Knowledge of current weed distribution and abundance is derived from multiple smaller studies, not a systematic study of maize weeds across a region.
Published studies of herbicide resistant weeds across the world are documented on a database. Estimates of weed species relative risks of evolving resistance were done in previous studies using those data. A list comprising thirty-nine common weeds associated with maize was generated from literature. Weeds were ranked for their risk of evolving herbicide resistance with a scoring protocol that accounts for the specific herbicides used in New Zealand maize. Seven weed species were classified as having a high risk of developing herbicide resistance: Echinochloa crus-galli (L.) P.Beauv., Chenopodium album, Eleusine indica (L.) Gaertn., Xanthium strumarium L., Amaranthus powellii S.Watson, Solanum nigrum L. and Digitaria sanguinalis. Seventeen species were classed as moderate risk and 15 were low risk. Herbicide classes associated with more resistant species were classed as high risk, these included acetohydroxy acid synthase (AHAS) inhibitors and photosystem-II inhibitors. Synthetic auxin herbicides had a moderate risk but only two herbicides in this class (dicamba and clopyralid) are registered for maize in New Zealand. All other herbicide mode-of-action groups used in maize were low risk. When accounting for herbicide groups used in maize, E. crus-galli, E. indica, C. album, D. sanguinalis and A. powelli were the five highest risk weeds.
Maize growers from two lists (Agribase and FAR) were called in random order for weed sampling. Thirty-six Waikato and sixteen Bay of Plenty maize fields were sampled prior to harvest, in late February-early March 2021. Weeds present were identified, and their percentage cover was estimated in two 133m transects. The first transect was in the ‘headland’, the area close to the field edge, and the second area in the centre of the maize field. Transect starting locations were randomized to minimize bias. Within each transect, six soil samples were taken at 33m intervals. Seeds were collected from individual plants throughout the field. As soon as possible, soil samples were taken back to the Ruakura glasshouse facility and germinated in trays. Seedlings were identified and enumerated, then soil was mixed; trays were assessed three times each. One-hundred and thirty-four plant species were observed in the fifty-two sampled sites in the field assessments and soil seedbanks. Digitaria sanguinalis (98%), Chenopodium album (85%) and Persicaria spp. (71%) were the most widespread weeds, with Setaria pumila, Sonchus oleraceus, Solanum nigrum, Erigeron spp. and Rumex obtusifolius seen in more than half of the farms. Digitaria sanguinalis, C. album, Persicaria spp., Cyperus rotundus, Echinochloa crus-galli had the highest percentage cover estimates, also common were Cynodon dactylon, Elytrigia repens, Paspalum distichum and Solanum nigrum. Winter and spring weeds Juncus bufonius, Poa annua and Stellaria media occurred frequently in soil seedbanks. A principal component analysis was done for weed percentage cover and weed seedbank densities for the fifty-two farms. For the percentage cover PCA C. album, C. rotundus, D. sanguinalis and Persicaria spp. were important taxa, and for the seedbank density PCA P. annua, J. bufonius, D. sanguinalis and S. media were important drivers of farm-farm compositional differences. Perennial weeds are a major problem in the eastern Bay of Plenty. Weeds with a history of evolved resistance C. album, P. maculosa and D. sanguinalis are common in both regions.
Earlier studies showed that Chenopodium album L. evolved atrazine and dicamba resistance in Waikato farms, Persicaria maculosa L. in Waikato and Digitaria sanguinalis (L.) Scop. in the Bay of Plenty and Waikato farms. Apart from atrazine resistant C. album - presumed omnipresent in New Zealand maize - the prevalence of resistant weeds was unknown in maize. This study was the first systematic survey to estimate the prevalence of herbicide resistant weeds in Bay of Plenty and Waikato maize. Of the fifty-two farms visited, thirty-two, thirty-one and twenty-nine had C. album, D. sanguinalis and Persicaria spp. (P. lapathifolia, P. maculosa) seed collected and tested for herbicide resistance, respectively. Persicaria spp. seedlings did not survive any herbicide treatments, of atrazine (1500 g.ai.ha-1), dicamba (600 g.ai.ha-1), nicosulfuron (60 g.ai.ha-1) and mesotrione (96 g.ai.ha-1). Chenopodium album seedlings were treated with the same rates of the same herbicides as Persicaria spp., and no C. album samples survived dicamba, nicosulfuron or mesotrione, but samples from twenty-two farms survived atrazine with no visible damage. Farms with atrazine-resistant C. album populations had C. album higher seedbank densities than farms with susceptible populations. Digitaria sanguinalis seedlings were treated with nicosulfuron (60 g.ai.ha-1). Ten farms had D. sanguinalis samples that survived, but three of those had low rates of survival. Even nicosulfuron resistant D. sanguinalis were stunted by the herbicide. A dose-response experiment to confirm and determine the level of resistance was set up, where plants from twelve farms were treated with 0, 15, 30, 60, 120, 240 g.ai.ha-1 nicosulfuron. Most resistant samples survived 60 g.ai.ha-1, but two survived up to 240 g.ai.ha-1. None of the six farms near the the first nicosulfuron resistant D. sanguinalis case had resistance, except for sites managed by the same contractor as the original site. Farms with nicosulfuron-resistant D. sanguinalis populations had significantly higher seedbank densities and percentage cover for D. sanguinalis compared to farms with susceptible populations. A total of twenty-four farms (46%) had a resistant weed, five of those had both nicosulfuron resistant D. sanguinalis and atrazine resistant C. album. Resistant C. album was detected across both regions, but was only in one eastern Bay of Plenty farm; resistant D. sanguinalis was sporadically distributed, but only detected in Waikato randomly sampled farms.
Results from the weed risk assessment show that more than half of species are at moderate-high risk of evolving herbicide resistance, but perennial weeds are less likely to evolve resistance. Commonly used photosystem-II inhibitors and AHAS inhibitors are high risk. The risk assessment may help maize growers avoid selecting for herbicide resistant weeds. The most observed weeds have either already evolved herbicide resistance (D. sanguinalis, C. album, P. maculosa) or were at high-risk of doing so (E. crus-galli). Perennial weeds are common in the eastern Bay of Plenty, especially C. rotundus. These weeds, and C. dactylon, E. crus-galli, E. repens, P. distichum and S. nigrum are abundant in fields. The most common weeds were tested for herbicide resistance, but only atrazine resistant C. album and nicosulfuron resistant D. sanguinalis were observed. Atrazine resistant C. album was common, in twenty-two farms (69% of tested farms, 42% of visited farms). No multiple-resistant C. album were detected. Nicosulfuron resistant D. sanguinalis was less common, in seven farms (23% of tested farms, 13% of visited farms). A similar proportion of resistant farms in Bay of Plenty-Waikato maize (46%) to Canterbury cereals (48%) was observed. Arable cropping is a repetitive environment that is highly selective for herbicide resistant, and tolerant, weeds. To prevent weeds from evolving herbicide resistance, integrated weed management practices are need. Chemical and non-chemical weed control strategies can reduce weed pressure and mitigate resistance evolution.
... The degree of herbicide resistance in a field is also closely correlated with the frequency of application 57 . This would be consistent with TSR mutations having been present already at low frequency before herbicides came into use, as shown through herbicide treatment of naive populations of Lolium rigidum 58 or the analysis of herbarium samples of A. myosuroides collected before the advent of modern herbicides 59 . In the case of L. rigidum, the frequency of sulfometuron-methyl resistance in previously untreated populations was around 10 -4 (ref. ...
... ) while among 685 A. myosuroides herbarium specimens, one individual collected nearly hundred years before the introduction of herbicides carried the ACCase Ile-1781-Leu mutation59 . We found TSR mutations in two of our three sensitive reference populations by deep amplicon sequencing (HerbiSeed standard, WHBM72 greenhouse standard APR/HA from Sep. 2014), although it is unknown when these populations were collected with respect to the relevant herbicides coming into broad use. ...
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.
