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Weed response to herbicides: Regional-scale distribution of herbicide resistance alleles in the grass weed Alopecurus myosuroides
New Phytologist
Abstract
Effective herbicide resistance management requires an assessment of the range of spatial dispersion of resistance genes among weed populations and identification of the vectors of this dispersion. In the grass weed Alopecurus myosuroides (black-grass), seven alleles of the acetyl-CoA carboxylase (ACCase) gene are known to confer herbicide resistance. Here, we assessed their respective frequencies and spatial distribution on two nested geographical scales (the whole of France and the French administrative district of Côte d'Or) by genotyping 13 151 plants originating from 243 fields. Genetic variation in ACCase was structured in local populations at both geographical scales. No spatial structure in the distribution of resistant ACCase alleles and no isolation by distance were detected at either geographical scale investigated. These data, together with ACCase sequencing and data from the literature, suggest that evolution of A. myosuroides resistance to herbicides occurred at the level of the field or group of adjacent fields by multiple, independent appearances of mutant ACCase alleles that seem to have rather restricted spatial propagation. Seed transportation by farm machinery seems the most likely vector for resistance gene dispersal in A. myosuroides.
... The spatial scale on which herbicide resistant genes evolve is still poorly understood; in fact, the majority of studies on resistance only consider one or a few weed populations (Menchari et al., 2006;Schulz et al., 2014;Matzenbacher et al., 2015;Babineau et al., 2017). To handle new weed outbreaks that are resistant to herbicides, or invasive and harmful weeds, farmers need spatial information that describes the location and the propagation, within and across fields, of the problematic weeds (Cardina et al., 1997). ...
... The average values are presented in the upper part of the bar, and in the lower part the significance of the comparison tests (different letters are significantly different, p ≤ 0.05). (Menchari et al., 2006;Schulz et al., 2014;Babineau et al., 2017). There have even been studies on the frequency of genes that confer resistance to ACCse in Alopecurus myosuroides, but they failed in detecting spatial structure in the distribution at all geographic scales (Menchari et al., 2006). ...
... (Menchari et al., 2006;Schulz et al., 2014;Babineau et al., 2017). There have even been studies on the frequency of genes that confer resistance to ACCse in Alopecurus myosuroides, but they failed in detecting spatial structure in the distribution at all geographic scales (Menchari et al., 2006). Kuester et al. (2015) agree that resistance evolved independently in each field, meaning that control of the species is more successful if done at the level of each field. ...
Echinochloa colona (L.) Link is one of the most troublesome weed species in rice (Oryza sativa L.) crops. Despite numerous cases of herbicide resistance in E. colona worldwide, in Colombia the reports are scarce and most of them dating from over two decades ago. To screen the resistance of E. colona to bispyribac-sodium, cyhalofop-butyl and quinclorac, in the Saldaña and Purificación counties, a survey was carried out in 23 rice fields, through a grid of 26 squares of 2.56 km 2 each. Seedlings from 23 populations were treated with commercial formulations from these respective herbicides at their recommended (1x) dose and twice the dose (2x) under controlled conditions. Relative fresh weight and percent control were evaluated. Populations with relative fresh weight greater than 20% and control below 80%, were categorized as resistant. For statistical analysis, a mixed model was used with populations as a random effect. The distribution of resistance was evaluated by a spatial autocorrelation analysis. It was established that 91% of populations were resistant to bispyribac-sodium, 48% to cyhalofop-butyl and 43% to quinclorac. Sixty-five percent had multiple resistance to two herbicides and 22% to three herbicides. Resistance was randomly distributed, according to the results obtained from the mixed model that showed a homogeneous response of populations within fields and heterogeneous among fields. This indicates that management strategies at field level generate a local selection pressure that determines the evolution of the resistance independently in each field.
... Thus, herbicide-resistant biotypes can extend quickly by the natural dispersal of seeds 11 and pollen. 12,13 On the other hand, the expansion of herbicide resistance in weeds can be related to agricultural practices such as the exchange of seeds and/or machinery between farms. 8 For instance, the littleseed canarygrass weed, Phalaris minor, was transported mixed with wheat seeds from Mexico to India. ...
... This study aimed (1) to determine the level of resistance in populations of A. fatua collected from BC and SON, (2) to determine which mutation accounts for herbicide resistance (the site of action involved in herbicide resistance) and (3) to describe the genetic structure and gene flow between populations, using microsatellite loci, which have proven to be useful for assessing whether population genetic structure and demographic processes are associated with resistance evolution. 12,13,21,22 In particular, we attempted to use molecular evidence to discern whether herbicide resistance in SON (the Valles de Hermosillo and Yaqui) evolved independently or resulted from migration from BC (Valle de Mexicali). Independent evolution would be suggested by genetic bottlenecks, low genetic diversity, reduced effective population size and lack of genetic structure between the Valle de Mexicali and Valle de Hermosillo populations. ...
... For instance, Alopecurus myosuroides plants resistant to ACCase inhibitors have contaminated organic farms. 12 Thus, pollen and seeds can disperse to surrounding areas under cultivation, changing the genetic structure of populations. Northern Mexico could be particularly vulnerable to herbicide-resistant biotypes introduced via dispersal from the United States, where herbicide resistance is highly prevalent. ...
Background:
Biotypes of Avena fatua resistant to ACCase-inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesized that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow, due to the transport and exchange of contaminated wheat seed. This study aimed to determine: 1) the resistance of A. fatua to ACCase-inhibiting herbicides in populations from BC and SON, 2) the mutation at the site of action and 3) the genetic structure and gene flow among populations.
Results:
DNA sequencing showed that all biotypes shared the same mutation (Leu x Ile at codon 1781). Microsatellites showed evidence of a genetic bottleneck in SON, and spatial analysis of molecular variance grouped one biotype from the Valle de Mexicali with two biotypes from the Valle de Hermosillo. Migration analysis suggested gene flow from the Valle de Mexicali to the Valle de Hermosillo, but not to the Valle del Yaqui.
Conclusions:
The presence of resistant biotypes of Avena fatua in the Valle de Hermosillo, SON are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds.
... The resistance evolved by repeated application of sethoxydim was endowed by a less sensitive form of ACCase [43], and therefore, resistance was attributed to target enzyme modifications. In other studies [44], frequencies of up to 99% of resistant ACCase alleles were observed in the field after 12 years of herbicide application, in agreement with our outcomes. However, although resistance evolves very rapidly over the landscape, a farmer may not quickly detect this problem because the number of adult plants was still low at simulation year four (20 plants/m 2 ). ...
... The initial frequency of resistance and large population sizes both resulted in resistance appearing during the first year of simulations in the seed bank of every field. Although [44] proposed multiple independent appearances of mutant ACCase alleles in a region as being the origin of the herbicide-resistant Alopecurus myosuroides populations rather than resistance dispersal, other studies show a more important role of the gene flow in resistance expansion [13]. In our model, the weed infestation was homogeneously distributed within the 1 ha field, but it is known that weeds are commonly grouped into patches, although L. rigidum populations do not usually show persistent patches over time [45]. ...
The repeated application of herbicides has led to the development of herbicide resistance. Models are useful for identifying key processes and understanding the evolution of resistance. This study developed a spatially explicit model at a landscape scale to examine the dynamics of Lolium rigidum populations in dryland cereal crops and the evolution of herbicide resistance under various management strategies. Resistance evolved rapidly under repeated herbicide use, driven by weed fecundity and herbicide efficacy. Although fitness costs associated with resistant plants reduced the resistance evolution, they did not affect the speed of its spread. The most effective strategies for slow resistance involved diversifying cropping sequences and herbicide applications. Pollen flow was the main dispersal vector, with seed dispersal also making a significant contribution. Strategies limiting seed dispersal effectively decreased resistance spread. However, the use of a seed-catching device at harvest could unintentionally enrich resistance in the area. It would be beneficial to optimize the movement of harvesters between fields. The model presented here is a useful tool that could assist in the exploration of novel management strategies within the context of site-specific weed management at landscape scale as well as in the advancement of our understanding of resistance dynamics.
... The resistance evolved by repeated application of sethoxydim was endowed by a less sensitive form of ACCase [44] and therefore it was resistance attributed to target enzyme modifications. In other studies [45] frequencies up to 99% of resistant ACCase alleles were observed at field after 12 years of herbicide application in agreement with our outcomes. However, although resistance evolved very rapidly over the landscape, a farmer may not detect this problem because the number of adult plants was still low at the simulation year four (20 plants/m 2 ). ...
... The initial frequency of resistance and large population sizes, both resulted in resistance appearing during the first year of simulations in the seed bank of every field. Although [45] proposed multiple independent appearances of mutant ACCase alleles in a region as the origin of the herbicide-resistant Alopecurus myosuroides populations rather than resistance dispersal, other studies show a more important role of the gene flow in resistance expansion [14]. In our model, the weed infestation was homogeneously distributed within the 1 ha field but it is known that weeds are commonly grouped into patches although L. rigidum populations do not usually show persistent patches over time [47]. ...
The repeated application of herbicides has led to the development of herbicide resistance. Models are useful for identifying key processes and understanding the evolution of resistance. This study developed a spatially explicit model at a landscape scale to examine the dynamics of Lolium rigidum populations in dryland cereal crops and the evolution of herbicide resistance under var-ious management strategies. Resistance evolved rapidly under repeated herbicide use, driven by weed fecundity and herbicide efficacy. Although fitness costs associated with resistant plants re-duced resistance evolution, they did not affect the speed of spread. The most effective strategies to slow resistance involved diversifying cropping sequences (e.g., crop rotation) and the herbicide applications (e.g., rotating different herbicide modes of action). Pollen flow was the main disper-sal vector, with seed dispersal also contributing significantly. Strategies limiting seed dispersal effectively decreased resistance spread. However, the use of a seed-catching device at harvest could unintentionally enrich resistance in the area. It would be beneficial to optimise the move-ment of harvesters between fields. The model presented here is a useful tool that may assist in the exploration of novel management strategies within the context of site-specific weed management at the landscape scale, as well as in the advancement of our understanding of resistance dynamics.
... Through haplotype analysis, it is possible to establish whether a point mutation shared among multiple populations emerged during a single selection process and then spread or if the resistance trait appeared via independent mutation events. This approach has been used to elucidate the evolution of resistance in several organisms (reviewed by Hawkins et al, 2019), 19 but only few studies are related to weeds, 20,21 and none on A. palmeri. Among the possible genetic variants, SNPs are normally preferred for population genetics and evolutionary studies. ...
... We did not use a highfidelity (HF) DNA polymerase because proofreading polymerases correct mismatches of allele-specific primers, thus eliminating primer specificity. 42 We opted for using an allele- 20 it is unlikely that the same mutation evolved independently in identical wild-type haplotypes, at least for the A. palmeri European populations described here. This is because A. palmeri is not native to Europe and is mainly reported as a casual alien species outside the agricultural habitat, 11 with populations that are normally very small compared to their native range. ...
BACKGROUND
Amaranthus palmeri is an aggressive annual weed native to the United States, which has become invasive in some European countries. Populations resistant to acetolactate synthase (ALS) inhibitors have been recorded in Spain and Italy, but the evolutionary origin of the resistance traits remains unknown. Bioassays were conducted to identify cross‐resistance to ALS inhibitors and a haplotype‐based genetic approach was used to elucidate the origin and distribution of resistance in both countries.
RESULTS
Amaranthus palmeri populations were resistant to thifensulfuron‐methyl and imazamox, and the 574‐Leu mutant ALS allele was found to be the main cause of resistance among them. In two Spanish populations, 376‐Glu and 197‐Thr mutant ALS alleles were also found. The haplotype analyses revealed the presence of two and four distinct 574‐Leu mutant haplotypes in the Italian and Spanish populations, respectively. None was common to both countries, but some mutant haplotypes were shared between geographically close populations or between populations more than 100 km apart. Wide genetic diversity was found in two very close Spanish populations.
CONCLUSION
ALS‐resistant A. palmeri populations were introduced to Italy and Spain from outside Europe. Populations from both countries have different evolutionary histories and originate from independent introduction events. ALS resistance then spread over short and long distances by seed dispersal. The higher number and genetic diversity among mutant haplotypes from the Spanish populations indicated recurrent invasions. The implementation of control tactics to limit seed dispersal and the establishment of A. palmeri is recommended in both countries. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
... Similarly, plants with the Trp2027Cys allele have lower seed production (Du et al., 2019;Menchari et al., 2008;Vila-Aiub et al., 2015). The frequencies of ACCase TSR mutations have been investigated in several studies 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). ...
... To tackle this question, we generated forward-in-time simulations with the software SLiM (Haller and Messer, 2019). While most studies focus on a few individuals of many populations (Délye et al., 2004c;Menchari et al., 2006), the depth of our pools allows us to assess more realistic haplotype frequencies of TSRs from our empirical data set ( Figure 3). We used high (0.7; Figure 5a,e), intermediate (0.4; Figure 5b,f) and low (0.1 and 0.05; Figure 5c,d,g,h) initial TSR frequencies for our simulations, considering that many TSRs are usually present in the heterozygous state. ...
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.
... Overall, the EO of P. somalensis showed more inhibitory activity against D. aegyptium than B. pilosa. This variation in the activity could be attributed to the genetic characteristics of the weeds [47]. ...
... Overall, the EO of P. somalensis showed more inhibitory activity against D. aegyptium than B. pilosa. This variation in the activity could be attributed to the genetic characteristics of the weeds [47]. The inhibitory activity of P. somalensis EO could be attributed to the high content of oxygenated terpenoid compounds, particularly sesquiterpenes (Table 1). ...
Pulicaria genus (fleabane) is characterized by its fragrant odor due to the presence of essential oil (EO). According to the literature reviews, the EO of Pulicaria somalensis O.Hoffm. (Shie) is still unexplored. For the first time, 71 compounds were characterized in EO derived from above-ground parts of P. somalensis collected from Saudi Arabia. Sesquiterpenes represented the main components (91.8%), along with minor amounts of mono-, diterpenes, and hydrocarbons. Juniper camphor (24.7%), α-sinensal (7.7%), 6-epi-shyobunol (6.6%), α-zingiberene (5.8%), α-bisabolol (5.3%), and T-muurolol (4.7%) were characterized as main constituents. The correlation analysis between different Pulicaria species showed that P. somalensis has a specific chemical pattern of the EO, thereby no correlation was observed with other reported Pulicaria species. The EO showed significant allelopathic activity against the weeds of Dactyloctenium aegyptium (L.) Willd. (crowfoot grass) and Bidens pilosa L. (hairy beggarticks). The IC50 value on the germination of D. aegyptium was double that of B. pilosa. The IC50 values on the root growth of B. pilosa and D. aegyptium were 0.6 mg mL−1 each, while the shoot growths were 1.0 and 0.7 mg mL−1, respectively. This variation in the activity could be attributed to the genetic characteristics of the weeds. Moreover, the EO exhibited significant antioxidant effects compared to ascorbic acid. Further studies are necessary to verify if these biological activities of the EO could be attributable to its major compounds.
... In-field surveys have been used to detect the presence of HR weeds at various geographical scales ranging from a single field (Preston and Powles, 2002), or the fields surrounding a single HR seed source (Falk et al., 2005) up to country level (Panozzo et al., 2013(Panozzo et al., , 2015a. Structured random or partially random surveys are generally used in relatively small (Menchari et al., 2006) and/or relatively large but homogeneous areas (not common in Europe, most used in the USA or Australia, see for example Owen et al., 2014). Surveys based on reported herbicide failures (also called complaint monitoring) are common and the aim is only to confirm the presence of resistance in sampled fields. ...
... Another approach, based on the identification of the seven mutations within the gene encoding the plastidic ACCase (acetyl-CoA carboxylase) was presented by Menchari et al. (2006) and Chauvel et al. (2006). They studied herbicide resistant A. myosuroides populations in France. ...
Long-term national European weed surveys, large scale classical phytosociological programs and camera-based documentation systems lead to results which can be documented in form of maps. Comparisons of these visual representations of relative weed positions can be used for the prediction of changing weed spectra and of plant biodiversity changes. Statistical methods connected with mapping software are used for the analysis of environmental factors and of farm managing practices influencing the occurrence of weeds. Maps produced by sensor-driven weed detection devices still differ considerably from maps produced via classical phytosociological approaches. Computer algorithms may allow the precise identification of some weeds in camera images. The present technical solutions are, however, still far from those achieved by experienced botanists. Many weed detection tools based on algorithms are not able to distinguish between closely related weeds yet. A few European countries have a long tradition of surveying weeds in major crops by traditional tools. Various software packages are employed for the analysis, documentation and visualisation of survey results. Large scale comprehensive maps including the infestation of crops over different countries are, however, often biased as not every national research group uses the same methods for the assessment of weed infestation. The ranking of the most common species seems, however, to allow comparable conclusions. The recognition of trends in spectrum changes can only be derived from long term studies as we see it. Our review reflects discussions within the Weed Mapping Working Group of the European Weed Research Society over the last ten years. We try to identify new research trends and to respond accordingly with new research projects. What we see today is a shift from traditional mapping approaches towards the use of digital devices as for example in precision farming projects. Another issue of increasing importance is the mapping of herbicide resistant biotypes.
... In Tasmania only (36%) of populations of ryegrass species had resistancethis was attributed to the lower cropping intensity (Broster et al. 2012). Similarly, in France surveys across large regions detected ACCaseresistant Alopecurus myosuroides in 50%-65% of the populations in winter wheat farms (Menchari et al. 2006). Multiple resistance in Avena fatua was found in 15%-50% of wheat fields in a regional survey of parts of Canada (Beckie et al. 2002(Beckie et al. , 1999. ...
... Multiple resistance in Avena fatua was found in 15%-50% of wheat fields in a regional survey of parts of Canada (Beckie et al. 2002(Beckie et al. , 1999. Published evidence suggests that the spread of resistant genotypes within fields (via seed or pollen) is common; however, resistance typically arises independently in individual farms (Menchari et al. 2006;Malone et al. 2013) via strong selection of rare resistant phenotypes which occur at ratios of 1:10,000-1:10,000,000 (Preston and Powles 2002;Neve 2008;Renton et al. 2014;Liu et al. 2017). Even in the absence of selection (i.e. ...
Herbicide resistance has repeatedly developed under intensive herbicidal weed management regimes globally with 255 species having resistant biotypes. In New Zealand, since 1979, resistance was found in 13 taxa, with >25 herbicides in 8 chemical classes showing reduced effectiveness (i.e. HRAC groups A, B, C, D, F, G, H, N and O). Cases included weeds in turf, pastures, orchards, vineyards, forage and arable crops. Surprisingly little is known about the spatial extent or frequency of this problem in New Zealand. We estimate that 14,000 farms have land-use histories like those favouring herbicide resistance historically. Sampling simulations of ≥10% farms provided good estimates of resistance prevalence for most regions and crop types. Acceptable sampling rates varied with target population size, actual resistance prevalence, and detection certainty. Our simulations provide a sobering caution regarding our ability to delimit the problem cheaply or accurately. Detection rates lower than 75% always give imprecise prevalence estimates. Sampling and screening involved 7.4 h labour and 27 km of travel costing 1 million NZD if lower risk farms were excluded, or >$3 million in exhaustive surveys. Regional farm and industry breakdowns could guide cost-sharing arrangements for surveys.
... Another reason À and one that has received less attention À is the synthetic, whole-organismal nature of weed science investigations more generally. For example, researchers studying the resistance problem will examine the phenotype by diagnosing the scale and extent of resistance among natural populations (Menchari et al., 2006;Kuester et al., 2015;Okada et al., 2015;D elye et al., 2016;Hicks et al., 2018), and will often pair this with a marker-assisted assessment of genetic differentiation and diversity to examine the likelihood that resistance alleles may migrate between areas via gene flow (Menchari et al., 2007;Okada et al., 2013Okada et al., , 2015Kuester et al., 2015;D elye et al., 2016). Furthermore, and often within the same herbicide-resistant species, researchers will investigate the genetic control of resistance (D elye, 2005;Powles & Preston, 2006;D elye et al., 2013aOkada & Jasieniuk, 2014;Scarabel et al., 2015) whether it is controlled by a single locus or is polygenicand will similarly identify both the genetic and physiological mechanism(s) responsible for resistance (reviewed in D elye et al., 2013a). ...
... A common question of interest in evolutionary biology is if the same adaptive phenotypes found among separate genetic lineages, populations, or species are due to parallel or nonparallel genetic changes (Losos, 2011;Martin & Orgogozo, 2013). As above, and as more explicitly reviewed in and D elye et al. (Menchari et al., 2006; or different species Tranel et al., 2018). Furthermore, the TSR mutations so far identified support the idea of 'extreme hotspots' of adaptation such that identical amino acid changes have independently evolved across separate species (Wood et al., 2005;Martin & Orgogozo, 2013). ...
The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide‐resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide‐resistant weeds in three broad areas – the genetic basis of adaptation, evolutionary constraints, experimental evolution – and similarly discuss questions left to be answered. I then develop how one would use herbicide‐resistance evolution as a model for studying eco‐evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide‐resistant plants as models for addressing key questions within ecology and evolution.
... The spatial structure of herbicide-resistant weeds has explored only TSR modeling by the evolution and spread of resistance alleles based on theoretical gene flow metrics (Cavan et al. 2000;Diggle et al. 2003;Maxwell et al. 1990;Menchari et al. 2006;Richter et al. 2002). Different models have correlated the spread of TSR alleles with the fitness differential between resistant and susceptible (Maxwell et al. 1990;Richter et al. 2002); therefore, the spatial structure from such models is species specific (or at least phylogenetically correlated). ...
... As many weeds show an aggregated (patchy) structure, it could be assumed that resistance will also show a patchy distribution. However, Menchari et al. (2006) found that ACCase herbicide-resistant alleles in blackgrass did not have a spatial structure and that the evolution of TSR resistance occurs at a small scale (field level). Using silky windgrass, Nordmeyer's (2009) model estimated the spread of TSR in the field but was unable to model the resistance allele dynamics in the absence of herbicide application. ...
Silky windgrass is a serious weed in central and northern Europe. Its importance has escalated in recent years because of its growing resistance to acetolactate synthase (ALS)-inhibiting herbicides. This study investigated the resistance level for three herbicide sites of action in eight silky windgrass populations, collected in fields neighboring a field where iodosulfuron sodium salt–resistant silky windgrass had previously been found. Target site resistance (TSR) and non–target site resistance (NTSR) mechanisms were identified, and a spatial gradient distribution hypothesis of ALS resistance was tested. Populations showed large variations in ED 50 values to iodosulfuron, with resistance indices (RIs) ranging from 0.1 to 372. No cross-resistance was found to other herbicide groups with the same site of action as iodosulfuron. In contrast, resistance was observed to the acetyl-CoA carboxylase inhibitor, fenoxaprop ethyl ester (RI from 0.7 to 776), while the activity of prosulfocarb, an inhibitor of long-chain fatty-acid synthesis, was unaffected. Iodosulfuron-resistant phenotypes were associated with NTSR, while fenoxaprop ethyl ester resistance was caused by both NTSR and TSR (Ile-1781-Leu mutation). A large-scale trend in the spatial distribution of resistance to ALS indicated a decreasing resistance with increased distance from an epicenter. After finer-scale analysis, less than 0.05% of the residual variation could be attributed to spatial autocorrelation. The spatial resistance pattern was not correlated with the dominant wind direction, while there was a correlation between the resistant phenotype and type of crop. This study underlines that NTSR mechanisms do not always confer broad resistance to different herbicide subclasses and site of action, hence the complex relationship to resistant phenotype. NTSR mechanisms, in particular detoxification, were present at different levels for the herbicides tested in the silky windgrass populations of this study. The factors contributing to the spatial distribution of resistance remain elusive.
... Several studies reported that Trp2027-Cys, Gly2096-Ala, and Ile2041-Asn mutation leads to resistance against APP herbicides while a mutation of Asp-2078-Gly caused resistance against APP as well as CHD herbicide group, which also includes clethodim (Beckie et al., 2000;Deĺye, 2005;Menchari et al., 2006;Liu et al., 2007;Yu et al., 2007;Kaundun, 2010). Some of the first reported mutations in P. minor's ACCase protein in the Mexico population are Asp-2078:Gly and Ile-1781:Leu, which is the probable reason for the loss in herbicides' affinity with the weed (Deĺye et al., 2008;Cruz-Hipolito et al., 2015;Raghav et al., 2016;Golmohammadzadeh et al., 2020). ...
Acetyl-CoA carboxylase (ACCase: EC 6.4.1.2) is one of the essential biotins containing enzymes required by plants for fatty acid synthesis and elongation. The unique enzyme is present in its homomeric form in all the Gramineae family, making it a suitable target for developing herbicides selectively against weeds of the Gramineae family. One such example infestation of Phalaris minor in winter wheat crop fields, where aryloxyphenoxypropionates (FOP); cyclohexanediones (DIM) and phenyl pyrazoline (DEN) group of ACCase inhibiting herbicides are used. However, the increasing number of ACCase herbicide resistant weed varieties has compelled agro-scientists to seek varied possibilities for weed control, through Integrated Weed Management (IWM) strategies. Developing new potential herbicides to regain sensitivity in weeds could be an approach to weed control. The current advancement in computational techniques could be of aid in developing new herbicide-like molecules by exploring the genomics, proteomics and structural details of catalytic sites of herbicide action in crops as well as weeds.
... Besides the decrease in high proportion of arable weeds, there are some species that have already adapted to more intensive farming conditions, and especially to herbicide inputs, in the case of Alopecurus myosuroides and some Lolium species [13][14][15]. As Storkey & Neve [16] stated there is an advantage of a diverse arable weed flora for economic and ecological reasons. ...
Former studies carried out in the 2000s in the Lahn-Dill region located in the middle-east of the German state Hesse stated a depletion of arable weeds on the field scale and more diverse weed flora on the landscape scale. Current study, having started in 2018, aims to contribute to a better understanding of the interactions between arable weed species diversity, farming intensity, grown crops and landscape area. Moreover, the potential of organic farming methods for conservation and promotion the arable weed diversity is aimed to be assessed with the study. In total, 42 fields in two landscape regions were sampled—six seedbank samples were collected from each field; additionally, data on spontaneous arable weed flora were recorded each spring from 2019 to 2021; emerged aboveground weeds were identified in the fields and their coverage was documented. Four factors were considered in the field trial: Farming practice, landscape area, soil depth and the current crop. Effects of these factors on arable weed species diversity were calculated with a Generalized Linear Model (GLM), resulting in significant effects of the management system, the area and the current crop. Among the four organic farming systems that were sampled, the time period of organic growing had a significant effect on weed seed numbers in the soil with an increase in seed numbers. Average seedbank species numbers were around twice as high in organic farming systems (18 species) compared to conventional managed fields (nine species). Evidence of an ongoing species decline in the region on the landscape scale could be detected by comparison with a former study. Especially rare and endangered weed species are a concern due to seedbank and current vegetation depletion tendencies.
... In 14 of these populations, we found different haplotypes with the same TSR mutation resulting from multiple independent mutation events, as opposed to the same TSR mutation being transferred to other haplotypes by recombination (Figure 4d, Supplementary extended data Figure 1). This observation confirms in an unbiased manner inferences from earlier explorative studies [45][46][47] . We also found seven instances in which two or three different TSR mutations had arisen in a single field, from the same haplotype (Figure 4b,c,e, Supplementary extended data Figure 1). ...
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.
... Although these genetic and ecological factors are fundamentally important for understanding the rate of adaptation of plant populations to herbicides and for tailoring appropriate resistance management guidelines, relatively few studies have explored regional-scale patterns of resistance frequency and dispersal or associated genetic and genomic signatures of resistance alleles. In Europe, studies focused on landscape-, national-and continentallevel patterns of resistance to acetyl CoA carboxylase (ACCase-) and acetolactate synthase (ALS-) inhibiting herbicides have implicated multiple, independent evolutionary origins of herbicide resistance alleles in weeds (Délye et al., 2010;Dixon et al., 2021;Menchari et al., 2006). Multiple origins of resistance for the ACCase-and ALS-inhibiting herbicide groups may be due in part to standing genetic variation for resistance to these herbicides (Délye et al., 2013), multiple possibilities for target-site mutations (Gaines et al., 2020) and the lack of large fitness costs for resistance to these herbicides (Vila-Aiub et al., 2009). ...
Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS-duplication genotypes, one having geographic associations with the Northern Plains and the other to the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.
... Alopecurus myosuroides was the second most abundant regulated quarantine species with four records, two of which occurred in Lolium perenne seed lots. Three of the records of Alopecurus myosuroides originated from France, a country where herbicide resistant biotypes of this species are known to be widespread [53]. Vegetable crop seeds accounted for thirteen unique seed lots with a regulated quarantine species, which was the most of any crop type (followed by forage with eight). ...
Imports of seeds for sowing are a major pathway for the introduction of contaminant seeds, and many agricultural weeds globally naturalised originally have entered through this pathway. Effective management of this pathway is a significant means of reducing future plant introductions and helps minimise agricultural losses. Using a national border inspection database, we examined the frequency, origin and identity of contaminant seeds within seed for sowing shipments entering New Zealand between 2014–2018. Our analysis looked at 41,610 seed lots across 1,420 crop seed species from over 90 countries. Overall, contamination was rare, occurring in 1.9% of all seed lots. Among the different crop types, the arable category had the lowest percentage of seed lots contaminated (0.5%) and the forage category had the highest (12.6%). Crop seeds Capsicum, Phaseolus and Solanum had the lowest contamination rates (0.0%). Forage crops Medicago (27.3%) and Trifolium (19.8%) had the highest contamination rates. Out of 191 genera recorded as contaminants, Chenopodium was the most common. Regulated quarantine weeds were the rarest contaminant type, only occurring in 0.06% of seed lots. Sorghum halepense was the most common quarantine species and was only found in vegetable seed lots. Vegetable crop seed lots accounted for approximately half of all quarantine species detections, Raphanus sativus being the most contaminated vegetable crop. Larger seed lots were significantly more contaminated and more likely to contain a quarantine species than smaller seed lots. These findings support International Seed Testing Association rules on maximum seed lot weights. Low contamination rates suggest industry practices are effective in minimising contaminant seeds. Considering New Zealand inspects every imported seed lot, utilises a working sample size 5 times larger than International Seed Testing Association rules require, trades crop seed with approximately half of the world’s countries and imports thousands of crop seed species, our study provides a unique overview of contaminant seeds that move throughout the seed for sowing system.
... Alopecurus myosuroides was the second most abundant regulated quarantine species with four records, two of which occurred in Lolium perenne seed lots. Three of the records of Alopecurus myosuroides originated from France, a country where herbicide resistant biotypes of this species are known to be widespread [53]. Vegetable crop seeds accounted for thirteen unique seed lots with a regulated quarantine species, which was the most of any crop type (followed by forage with eight). ...
Imports of seeds for sowing are a major pathway for the introduction of contaminant seeds, and many agricultural weeds globally naturalised originally have entered through this pathway. Effective management of this pathway is a significant means of reducing future plant introductions and helps minimise agricultural losses. Using a national border inspection database, we examined the frequency, origin and identity of contaminant seeds within seed for sowing shipments entering New Zealand between 2014-2018. Our analysis looked at 41,610 seed lots across 1,420 crop seed species from over 90 countries. Overall, contamination was rare, occurring in 1.9% of all seed lots. Among the different crop types, the arable category had the lowest percentage of seed lots contaminated (0.5%) and the forage category had the highest (12.6%). Crop seeds Capsicum, Phaseolus and Solanum had the lowest contamination rates (0.0%). Forage crops Medicago (27.3%) and Trifolium (19.8%) had the highest contamination rates. Out of 191 genera recorded as contaminants, Chenopodium was the most common. Regulated quarantine weeds were the rarest contaminant type, only occurring in 0.06% of seed lots. Sorghum halepense was the most common quarantine species and was only found in vegetable seed lots. Vegetable crop seed lots accounted for approximately half of all quarantine species detections, Raphanus sativus being the most contaminated vegetable crop. Larger seed lots were significantly more contaminated and more likely to contain a quarantine species than smaller seed lots. These findings support International Seed Testing Association rules on maximum seed lot weights. Low contamination rates suggest industry practices are effective in minimising contaminant seeds. Considering New Zealand inspects every imported seed lot, utilises a working sample size 5 times larger than International Seed Testing Association rules require, trades crop seed with approximately half of the world’s countries and imports thousands of crop seed species, our study provides a unique overview of contaminant seeds that move throughout the seed for sowing system.
... As costs of DNA sequencing and tests decrease, there also could be a point where genetic tests may be less expensive than physical screening. Herbicide resistance surveys focussing on specific mutations have been conducted across cropping regions in France 33,78 and Australia. 48,79 However, additional time would be needed to allow testing across a range of resistance mechanisms for multiple populations and species. ...
The scale of herbicide resistance within a cropping region can be estimated and monitored using surveys of weed populations. The current approach to herbicide resistance surveys is time‐consuming, logistically challenging and costly. Here we review past and current approaches used in herbicide resistance surveys with the aims of (i) defining effective survey methodologies, (ii) highlighting opportunities for improving efficiencies through the use of new technologies and (iii) identifying the value of repeated region‐wide herbicide resistance surveys. One of the most extensively surveyed areas of the world's cropping regions is the Australian grain production region, with >2900 fields randomly surveyed in each of three surveys conducted over the past 15 years. Consequently, recommended methodologies are based on what has been learned from the Australian experience. Traditional seedling‐based herbicide screening assays remain the most reliable and widely applicable method for characterizing resistance in weed populations. The use of satellite or aerial imagery to plan collections and image analysis to rapidly quantify screening results could complement traditional resistance assays by increasing survey efficiency and sampling accuracy. Global management of herbicide‐resistant weeds would benefit from repeated and standardized surveys that track herbicide resistance evolution within and across cropping regions. © 2021 Society of Chemical Industry.
... The emergence of pesticide resistance in agricultural ecosystems is a hallmark system for investigating convergent evolution at the molecular and population genetic level (Baucom, 2019;Hawkins et al., 2019). In weeds evolving resistance to herbicides, often the same genetic changes are observed across lineages of the same species (Menchari et al., 2006;Powles & Yu, 2010). The underlying mutations are mostly focused on the gene encoding a key enzyme being perturbed by a given herbicide. ...
Convergent evolution leads to identical phenotypic traits in different species or populations. Convergence can be driven by standing variation allowing selection to favour identical alleles in parallel or the same mutations can arise independently. However, the molecular basis of such convergent adaptation remains often poorly resolved. Pesticide resistance in agricultural ecosystems is a hallmark of convergence in phenotypic traits. Here, we analyse the major fungal pathogen Zymoseptoria tritici causing serious losses on wheat and with fungicide resistance emergence across several continents. We sampled three population pairs each from a different continent spanning periods early and late in the application of fungicides. To identify causal loci for resistance, we combined knowledge from molecular genetics work and performed genome‐wide association studies (GWAS) on a global set of isolates. We discovered yet unknown factors in azole resistance including a gene encoding membrane associated functions. We found strong support for the “hotspot” model of resistance evolution with convergent changes in a small set of loci but additional loci showed more population‐specific allele frequency changes. Genome‐wide scans of selection showed that half of all known resistance loci were overlapping a selective sweep region. Hence, the application of fungicides was one of the major selective agents acting on the pathogen over the past decades. Furthermore, loci identified through GWAS showed the highest overlap with selective sweep regions underlining the importance to map phenotypic trait variation in evolving populations. Our population genomic analyses highlighted that both de novo mutations and gene flow contributed to convergent pesticide adaptation.
... Consistent with the present results, the EO from aboveground parts of Pulicaria somalensis has been reported to have a stronger allelopathic effect on D. aegyptium than B. pilosa [10]. This could be attributed to the genetic resistance of weeds [48]. ...
Plants are considered green resources for thousands of bioactive compounds. Essential oils (EOs) are an important class of secondary compounds with various biological activities, including allelopathic and antimicrobial activities. Herein, the present study aimed to compare the chemical profiles of the EOs of the widely distributed medicinal plant Calotropis procera collected from Saudi Arabia and Egypt. In addition, this study also aimed to assess their allelopathic and antimicrobial activities. The EOs from Egyptian and Saudi ecospecies were extracted by hydrodistillation and analyzed via GC-MS. The correlation between the analyzed EOs and those published from Egypt, India, and Nigeria was assessed by principal component analysis (PCA) and agglomerative hierarchical clustering (AHC). The allelopathic activity of the extracted EOs was tested against two weeds (Bidens pilosa and Dactyloctenium aegyptium). Moreover, the EOs were tested for antimicrobial activity against seven bacterial and two fungal strains. Ninety compounds were identified from both ecospecies, where 76 compounds were recorded in Saudi ecospecies and 33 in the Egyptian one. Terpenes were recorded as the main components along with hydrocarbons, aromatics, and carotenoids. The sesquiterpenes (54.07%) were the most abundant component of EO of the Saudi sample, while the diterpenes (44.82%) represented the mains of the Egyptian one. Hinesol (13.50%), trans-chrysanthenyl acetate (12.33%), 1,4-trans-1,7-cis-acorenone (7.62%), phytol (8.73%), and myristicin (6.13%) were found as the major constituents of EO of the Saudi sample, while phytol (38.02%), n-docosane (6.86%), linoleic acid (6.36%), n-pentacosane (6.31%), and bicyclogermacrene (4.37%) represented the main compounds of the Egyptian one. It was evident that the EOs of both ecospecies had potent phytotoxic activity against the two tested weeds, while the EO of the Egyptian ecospecies was more effective, particularly on the weed D. aegyptium. Moreover, the EOs showed substantial antibacterial and antifungal activities. The present study revealed that the EOs of Egyptian and Saudi ecospecies were different in quality and quantity, which could be attributed to the variant environmental and climatic conditions. The EOs of both ecospecies showed significant allelopathic and antimicrobial activity; therefore, these EOs could be considered as potential green eco-friendly resources for weed and microbe control, considering that this plant is widely grown in arid habitats.
... A number of previous studies have explored genetic variation, population structure and diversity of herbicide TSR alleles in Alopecurus myosuroides, generally concluding that (i) genetic diversity within populations is high, (ii) differentiation between populations is low, (iii) evolution of resistance has not reduced genome-wide patterns of genetic diversity and (iv) resistance evolves as multiple independent events, though with some localized dispersal of resistance alleles via gene flow. 10,[16][17][18] In this study, we explore patterns of genetic variation using 20 426 single-nucleotide polymorphisms (SNPs) and a sample of 369 blackgrass individuals from 47 fields across the British Isles to test if spatial patterns of population structure are consistent with general expectations under rapid range expansion [i.e. isolation by distance (IBD], allele frequency gradients along major vectors of migration and reduced diversity in more recently colonized areas [19][20][21]. ...
BACKGROUND
Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping‐by‐sequencing and population‐level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome‐wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance.
RESULTS
Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site‐associated DNA (RAD)‐sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (FST = 0.024–0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (FIS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population‐level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers.
CONCLUSION
There is likely extensive human‐mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry
... There are currently genetic marker assays in some species of managed weeds for genes that confer herbicide resistance. For example, alleles of acetyl-CoA carboxylase (ACCase; Menchari et al. 2006) and phytoene desaturase (Benoit and Les 2013) are known to confer resistance to ACCase-inhibiting herbicides and fluridone (1-methyl-3-phenyl-5-[3-(trifluromethyl) phenyl]-4(1H)-pyridinone), respectively. Copy number of 5-Enolypyruvyl-shikamate-3-phosphate synthase can also be used to determine resistance to glyphosate (Chatham et al. 2015). ...
Genetic assays to identify herbicide resistant plants are a promising tool to reduce herbicide failures. However, the genetic basis of herbicide resistance is frequently unknown. In clonal weed species, DNA fingerprinting could be a useful tool to identify known resistant versus susceptible genets (clones) that occur in multiple locations, without an immediate need for understanding the genetic mutation(s) conferring resistance. Eurasian watermilfoil ( Myriophyllum spicatum L.) is a mostly clonal invasive aquatic plant, and the same clones can be found in multiple waterbodies. Previously, a clone was confirmed as resistant to the commonly used herbicide, fluridone, and a recent genetic survey in Michigan identified this genotype (MG-237) in at least seven other lakes. We hypothesized MG-237 collected from different lakes would also exhibit fluridone resistance. However, MG-237 may have accumulated resistance mutations at different times during its spread across Michigan, resulting in fluridone resistant and susceptible MG-237 clones distributed in different lakes. We used an herbicide assay to test the response of several accessions, including MG-237 accessions from multiple lakes, to the Michigan operational rate of 6 µg L ⁻¹ fluridone. We found that all accessions of MG-237 exhibited resistance to 6 µg L ⁻¹ fluridone. A second genotype (MG-377) was also resistant to 6 µg L ⁻¹ fluridone. The rest of the accessions were found to be significantly injured by 6 µg L ⁻¹ fluridone. Our results suggest that 6 µg L ⁻¹ fluridone would not effectively control waterbodies dominated by MG-237 or MG-377, whereas waterbodies dominated by the other genotypes in our study would likely be controlled. Although more studies are needed to identify the variation in sensitivity of the accessions tested here, and the genetic basis of fluridone resistance in watermilfoil, our results suggest that multilocus genotype data may be an effective tool to identify and track herbicide-resistant genotypes of watermilfoil in the short-term.
... The potential emergence of herbicide-resistant biotypes is also a future threat that needs monitoring. Evolved herbicide resistance has been observed in many grass weeds, including A. myusoroides (Menchari et al., 2006) and V. bromoides (Heap, 2020), and could appear in V. myuros with time if the species invades more cropping systems and is increasingly targeted by herbicide treatments. ...
Vulpia myuros is an annual grass species of Mediterranean origin, which has achieved
a global distribution. It is a fast-growing species, with high colonisation and competitive
abilities. This species is considered an invasive weed in most countries where it
has been introduced, with highly negative economic impact where it now dominates.
It is increasingly found to be a problematic weed in winter cereals, especially in notill
and reduced tillage systems, across Europe, United States and Australia. Seeds
of V. myuros have reduced germination potential when buried. However, where tillage
interventions are reduced, ideal conditions for V. myuros are created. Minimum
and no tillage practices are increasing worldwide, with a concomitant increase in the
spread and abundance of V. myuros. Effectiveness of herbicides is mostly suboptimal,
in particular for well-established populations forming dense swards, even though no
herbicide resistance has yet been identified. An integrated management approach,
increasing crop diversification combined with management adaptations, possibly including
herbicides is suggested as an effective control strategy. Despite increasing
research on V. myuros, more information is needed to optimise the management of
this weed. Based on the species’ Mediterranean origins and adaptation to warm and
dry environments, an increase of its global importance may be expected with climate
changes. It is thus paramount to increase the awareness around this species, improve
its identification in the field and monitor its spread before it becomes a concern of
similar magnitude to grass weeds like Alopecurus myosuroides or Lolium rigidum.
... What's more, ad-hoc reporting may reflect strong biases towards a small number of the most problematic weeds. With some notable exceptions, particularly in cropping systems in Australia [12][13][14][15][16][17], systematic surveys to detect herbicide resistance cases are rare, and often focus on one or two problematic species in a given crop, for example, Alopecurus myosuroides Huds. in French wheat fields [18] or Avena fatua L. in two Canadian townships [19]. Systematic surveys may be rare because of the cost, a lack of specific pathways for reporting [11], and industry perceptions about the importance of resistance. ...
We estimated the risk of selecting for herbicide resistance in 101 weed species known to occur in wheat and barley crops on farms in New Zealand. A protocol was used that accounts for both the risk that different herbicides will select for resistance and each weed’s propensity to develop herbicide resistance based on the number of cases worldwide. To provide context we documented current herbicide use patterns. Most weeds (55) were low-risk, 30 were medium-risk and 16 high-risk. The top ten scored weeds were Echinochloa crus-galli, Poa annua, Lolium multiflorum, Erigeron sumatrensis, Raphanus raphanistrum, Lolium perenne, Erigeron bonariensis, Avena fatua, Avena sterilis and Digitaria sanguinalis. Seven out of ten high-risk weeds were grasses. The most used herbicides were synthetic auxins, an enolpyruvylshikimate-phosphate synthase inhibitor, acetolactate synthase (ALS) inhibitors, carotenoid biosynthesis inhibitors, and long-chain fatty acid inhibitors. ALS-inhibitors were assessed as posing the greatest risk for more species than other modes-of-action. Despite pre-emergence herbicides being known to delay resistance, New Zealand farmers only applied flufenacet and terbuthlazine with high frequency. Based on our analysis, surveys for herbicide-resistant species should focus on the high-risk species we identified. Farmer extension efforts in New Zealand should address resistance evolution in cropping weeds.
... Cette population peut donc être considérée comme représentative de la diversité allélique d'ACCase "pré-herbicide", donc "pré-sélection". Grâce à cette population, il a été montré que la sélection positive qui cible les quelques mutations codantes impliquées dans la résistance aux herbicides apparaît environ 15 générations après le début des traitements (Menchari et al., 2006). L'utilisation des herbicides, bien que très récente, a donc clairement un effet visible sur la variation génétique du gène codant pour l'ACCase. ...
L'objectif de cette étude est de décrire puis analyser et comparer le polymorphisme de séquence des gènes eIF4E (eukaryotic Initiation Factor 4E) de résistance aux potyvirus, afin de mettre en relation ce polymorphisme avec la double fonction des protéines eIF4E dans les processus cellulaires de l'hôte et dans l'interaction avec les potyvirus. La stratégie repose sur l'association d'analyses fonctionnelles et d'études d'évolution moléculaire des gènes eIF4E chez deux Solanacées (piment et tomate) et chez l'espèce modèle Arabidopsis thaliana. En ce qui concerne le rôle de eIF4E dans les processus cellulaires, la pression de sélection purificatrice forte identifiée pour l'ensemble des gènes eIF4E argumente en faveur de l'acquisition d'une spécialisation fonctionnelle, et ce bien que toutes les protéines eIF4E apparaissent capables de complémenter une levure délétée de son gène eIF4E. En ce qui concerne le rôle de eIF4E dans les interactions plantes-potyvirus, une importante diversité de variants alléliques a été identifiée au locus eIF4E1-pvr2 du piment, diversité caractérisée par des substitutions nucléotidiques exclusivement non-synonymes. La plupart de ces substitutions, impliquées dans la résistance aux PVY (Potato virus Y) et TEV (Tobacco etch virus) via une modification de l'interaction avec la protéine virale VPg (Viral Protein genomelinked), sont sous pression de sélection positive. Ces résultats couplés à ceux montrant que des mutations dans la VPg permettent aux potyvirus de s'adapter aux protéines eIF4E1 de résistance, mettent en évidence l'existence d'une coévolution entre eIF4E1 et VPg. Cette coévolution n'est cependant pas retrouvée chez la tomate et A. thaliana, indiquant que leurs caractéristiques biologiques d'interaction avec les potyvirus "in natura" conduisent à des profils différents d'évolution des gènes eIF4E. Plus globalement, ces résultats associés à ceux montrant la conservation de la position des substitutions en acides aminés dans les protéines eIF4E de résistance d'espèces très éloignées suggèrent l'existence d'une évolution convergente
... A third reason for tillage is the control of weeds, diseases and pests. Blackgrass (Alopecurus myosuroides Huds.) is the most serious weed problem in winter wheat in the UK, particularly on wet clay soils (Colbach and Sache, 2001;Chauvel et al., 2001;Menchari et al., 2006). There are also herbicide-resistant populations of blackgrass in England (Moss, 2013), and hence one of the key ways of controlling the weed is through a crop rotation that includes non-cereal crops. ...
... Studies indicate that target site mutations are a common mechanism of providing resistance to ACCase-inhibiting herbicides in grasses in Iran and rigid ryegrass in South Australia (Zand et al., 2006;Malone et al., 2010). Other studies on ACCase-resistant A. myosuroides in France have reported resistance without mutation in ACCase ( Menchari et al., 2006 andDélye et al., 2007). The current study showed that two mutations led to resistance to ACCase- inhibiting herbicides in resistant rigid ryegrass biotypes, an Ile-2041-Asn mutation (in eight biotypes) and an Ile-178-Leu mutation (in two biotypes). ...
Weed competition, especially from grass species, is estimated to cause 23% reduction in yield in the wheat fields of Iran. During the years 2013 to 2016, a study was conducted to evaluate the resistance to herbicides of 30 rigid ryegrass (Lolium rigidum) biotypes that had been collected from wheat fields of Khuzestan Province. The screening of these biotypes was conducted with clodinafop-propargyl in the greenhouse and revealed biotypes with a survival rate of greater than 20% in response to this herbicide. These biotypes were further studied for the evaluation of cross and multiple resistance. A total of 94 and 75% of the rigid ryegrass biotypes showed resistance to ACCase-and ALS-inhibitors, respectively. Approximately 69% of the rigid ryegrass biotypes included individuals with resistance to at least two herbicide mechanisms of action. This is the first report of cross and multiple resistance in rigid ryegrass biotypes from Iran. The leaves of the rigid ryegrass biotypes cross-resistance to ACCase-inhibitors were analyzed using CAPS and dCAPS markers to identify probable amino acid substitutions at 2,041, 2,088, 1,781, and 2,078 positions on the ACCase gene. In two and nine biotypes, mutations were observed in the 1,781 and 2,041 positions, respectively. These results indicated that there is a serious problem with herbicide resistance in rigid ryegrass, including cross and multiple resistance, and a need to implement long-term integrated management strategies.
... Délye et al. (2004) used phylogenetic analysis of the ACCase sequence in nine populations of the grass weed, A. myosuroides to demonstrate that there had been four and six independent origins of the L1781I and N2041I substitutions, respectively, across nine populations of the species. Further ACCase sequencing over a larger set of A. myosuroides populations in France identified L1781, N2041 and A2096 haplotypes differing by up to eight, 11 and 10 mutations, respectively (Menchari et al., 2006), further supporting multiple independent origins. These studies did not explore signatures of selection around resistance-conferring loci to infer whether mutations arose from standing genetic variation or by de novo mutation. ...
Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre‐existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target‐site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non‐chemical pest‐control methods.
... Manipulative field experiments 60,61 and field observations of gene flow between herbicide-resistant and -susceptible crop varieties have been conducted. 62 Population genetics analyses have used the sequence and/or frequency of herbicide target genes, 63 amplified fragment length polymorphism (AFLP) markers 64 and microsatellites/simple sequence repeats. 65,66 With access to less expensive sequencing technologies, it becomes possible to generate orders of magnitude more data (tens of thousands of markers) for genotyping-by-sequencing and population genomics studies. ...
There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the ‘state of the art’ in genomics and weed genomics, including technologies, applications, and on‐going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research.
... Previous population genetics studies investigating the phylogeographic structure of pesticide resistant organisms reveal either a single origin (Raymond and Callaghan, 1991;Linda and Alan, 1997;Daborn et al., 2002) or, more frequently, redundant independent, parallel evolution events shaped by variations in selection pressure (Cavan et al., 1998;Anstead et al., 2005;Menchari et al., 2006;Chen et al., 2007;Pinto et al., 2007;Délye et al., 2010). As an example, it was found that glyphosate resistance in horseweed (Conyza canadensis) from California had multiple independent origins within the Central Valley and evolved many years before its first detection. ...
Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.
... One of the most comprehensive recent European surveys of resistant A. myosuroides came from the wheat growing areas of northern France in 2006 (Menchari et al., 2006). This work, supported by the local growers' cooperative, went further than most large scale surveys in that it addressed the spatial distribution of seven different resistant alleles of the acetyl-CoA carboxylase (ACCase) gene on two different geographical scales. ...
... Pollen loads on the filter were crushed for 30 s with 30 µL of a buffer solution (100 nM Tris-HCl, pH 9.5, 1 M KCl and 10 mM EDTA) using a rotary pestle, following the DNA extraction protocol from Menchari et al. (2006). The Eppendorf ® microtube was held in an ice bath during this step, then placed in a thermo-cycler (ThermoStat Plus, Eppendorf) at 95 °C for 9 min and put back on ice for 5 min. ...
Faced with the decline of pollinators, it is relevant to strengthen our understanding of the whole plant-pollinator web in semi-natural grasslands that serve as refuges for pollinator populations. The aim of this study was to explore the diversity of flower-foraging insects involved in pollen transfer in mountain semi-natural grasslands. Insects actively collecting pollen and/or nectar were caught in spring in six mountain semi-natural grasslands displaying a floristic richness gradient. Individual determinations of insects were made at the finest possible taxonomic scale and pollen loads were removed from the insect body. Using next-generation DNA sequencing, pollens were identified through the ribosomal DNA cistron using the ITS2 database and the ITS plant rDNA cistron sequences from Genbank. A total of 236 flower-foraging insects were collected. Diptera represented 82% of the total catches distantly followed by Hymenoptera (15%) and Apoidea (bees) (11%). Visual observations revealed that Diptera foraged on 16 of the 21 flower species visited by insects. DNA metabarcoding showed that 82% (191) of all of the collected insects were carrying pollen and 44% (104) were carrying two genera of plants or more. Our results demonstrate that Diptera are potential key-pollinators in mountain semi-natural grasslands that cannot be overlooked by the scientific community. However difficulties of taxonomic determination due to severe shortage of experts for Diptera have to be urgently overcome. Further studies on the link between pollen transfer and actual pollination in a global change context are also required. Moreover, our results support the idea that DNA metabarcoding provides accurate information about the plants-insects networks but it also pointed out sensitive issues, especially the necessity to build reliable national barcode databases.
... Alopecurus myosuroides containing 1781Leu/ Leu ACCase also showed a fitness advantage in seed germination (Délye et al., 2013). In addition, wide spread of Ile1781Leu ACCase in L. rigidum and across grass species may suggest that Ile1781Leu ACCase usually cause no fitness cost (Délye et al., 2005;Zhang and Powles, 2006;Menchari et al., 2006;Liu et al., 2007;Yu et al., 2007). In this paper, seeds containing homozygous 1781Leu/Leu ACCase showed a fitness advantage under salt and osmotic stress, but no fitness variation in optimal experimental condition. ...
American slough grass (Beckmannia syzigachne Steud. Fernald) is an annual grass which has developed resistance to acetyl-coenzyme A carboxylase (ACCase) inhibitors, and the major mechanism of resistance is target site based. Target site resistance-conferring mutations may confer pleiotropic effects on a weed's life cycle. The effects of three American slough grass spontaneous ACCase mutations (Ile1781Leu, Trp2027Cys and Ile2041Asn) on seed germination and viability under different experimental factors had been investigated in this paper. Seeds containing homozygous 1781Leu/Leu ACCase showed a greater germination under salt and osmotic stress, but no fitness variation in optimal experimental conditions. Homozygous 2027Cys/Cys ACCase caused nonsignificant effects on seed germination in optimal experimental conditions, but caused a greater germination after 16 d incubation at 40 °C and 100% RH. Homozygous 2041Asn/Asn ACCase tended to cause nonsignificant effects on seed germination or seed viability. Finally, an obvious population effects on seed germination was observed between six subpopulations, which indicated that fitness assessing should be measured in resistant and susceptible individuals that share a similar genetic background. These findings suggest that the absence of fitness penalty associated with these three homozygous mutant ACCase alleles may be a contributing factor for resistance spread.
... DÉLYE et al. (2007) detected a strong relationship between the frequency of use of ACCase inhibitors and an increasing number of resistant black-grass biotypes. The powerful selective pressure targeting a single gene or a few genes is consequently expected to rapidly increase the frequency of mutation conferring the adapted phenotypes (MENCHARI et al., 2006;MARECHAL et al., 2009;PETIT et al., 2010). This is why we started the investigations of the impact of imazamox containing herbicides on the development of resistance in black-grass. ...
Winter oilseed-rape was the most common crop in Western Europe where no ALS-inhibitor was used. Due to the introduction of Clearfield winter oilseed-rape varieties the use of ALS-inhibitors also in oilseed-rape is possible. If the broader use of ALS-inhibitors increases the selection pressure on herbicide resistant weeds and increases their occurrence in the crop rotation is the question of this investigation. Therefore, an outdoor container trial (á 350 l, 0.7 m²) was performed starting in autumn 2011. A typical crop rotation of winter wheat/oilseed-rape/winter wheat was simulated in the following three years. Three different black-grass biotypes with characterised resistance pattern and 5 different herbicide programs were analysed. The blackgrass biotypes showed different target-site resistance against ACCase- and/or ALS-inhibitor, as well as metabolic resistance. Before and after each treatment the numbers of black-grass plants per container were counted. Also the numbers of heads were counted before harvest. Additionally genetic analysis due to PCRs and pyrosequencing of ten survivors per container and year were performed.
Till now results of the winter wheat and oilseed-rape cultivation were obtained. Herbicide efficacy was between 77 and 98% for the treatments during the winter wheat cultivation. The genetic analysis showed nearly similar portion of TSR in the black-grass populations when compared with the initial frequencies. Only one container showed no TSR.
The comparison of the herbicide programs sprayed during the oilseed-rape cultivation showed the best results for all black-grass biotypes for the application of: Metazachlor + dimethenamid (BBCH 09/10), imazamox + quinmerac + Dash (BBCH 14) and propyzamide (BBCH 21/22).
... Within the carboxyl-transferase (CT) domain of the plastidic ACCase gene, published markers were used to detect L1781 and N2041 mutations. In previous studies, these mutations are the most frequently observed in different grass weed species [19,20]. ...
... Plant defense is generally hypothesized to involve a cost. This expectation stems from the surprising observation of genetic variation underlying plant defense traits in many natural systems, whether the elicitor of damage is an herbivore, a pathogen, or an herbicide Rausher 1987, 1989;Stahl et al. 1999;Baucom and Mauricio 2004;Bakker et al. 2006;Menchari et al. 2006;Délye et al. 2010;Kuester et al. 2015). If there were no costs associated with defense, alleles conferring either resistance or tolerance to damage should increase to fixation rendering all individuals in the population highly defended . ...
Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here we examine the potential for life-history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life-history trade-offs associated with all three traits; highly resistant populations had lower germination, shorter roots and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments. This article is protected by copyright. All rights reserved.
... The principal advantage of quantitative molecular-resistance diagnosis assays over all other types of assay is their very low detection threshold (reviewed for insecticide resistance in [70]). They may allow the detection of resistant genotypes in a pest population sufficiently early Genotyping (Known) Mutations by DNA Amplification or Ligation Detection 'Low-tech' PCR-derived mutation genotyping D/Q SNPs, indels Cheap, simple, basic technical requirements Adaptation to high-throughput requires equipment PCR-RFLP/CAPS, PIRA-PCR/ dCAPS Allele-specific PCR [131][132][133][134][135][136] [92, 137,138] 'Hi-tech' PCR-derived mutation genotyping D/Q SNPs, indels High-throughput, allows sample pooling Requires costly equipment and reagents, calibration for quantification MALDI-TOF/Sequenom® MassARRAY HRM, SimpleProbe ® melting curve analysis SNuPE (SNaPshot TM ) ASPPAA, KASPar-qPCR TM , ARMS/Scorpion®, TaqMan® [139][140][141] [142-144] [145,146] [147][148][149][150][151][152][153] Oligonucleotide ligation Assay D/Q SNPs, indels Cheap, rapid, highthroughput possible Adaptation to high-throughput requires equipment OLA, HOLA, SOTLA [154,155] Isothermal amplification D/Q SNPs, indels Cheap and rugged, highthroughput possible Adaptation to high-throughput or quantification requires equipment; complex assay design LAMP [156][157][158] D/Q SNPs, indels High-throughput; detection of numerous resistance mutations; allows sample pooling Relevant only for large samplings; requires costly equipment or subcontracting, downstream bioinformatics analysis Quantification must take the ploidy of the species and sequencing error rate into account PCR followed by pyrosequencing, 454, or Illumina sequencing [66,159,160] ...
Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides whilst maintaining pesticide efficacy. This goal requires monitoring of the emergence and development of resistance to pesticides in crop pests. To this end, various methods for resistance diagnosis have been developed for different groups of pests. This review provides an overview of biological, biochemical and molecular methods that are currently used to detect and quantify pesticide resistance. The agronomic, technical and economic advantages and drawbacks of each method are considered. Emerging technologies are also described, with their associated challenges and their potential for the detection of resistance mechanisms likely to be selected by current and future plant protection methods.
... The distribution of herbicide resistance alleles can appear at random, suggesting multiple, independent appearances of the mutations or by pollen mediated gene flow from a single individual population or area [6,39]. This gene flow increases the initial frequency of herbicide resistance alleles in unselected L. rigidum populations [14,40]. ...
The transfer of herbicide resistance genes by pollen is a major concern in cross-pollinated species such as annual ryegrass (Lolium rigidum). A two-year study was conducted in the greenhouse, under favorable conditions for pollination, to generate information on potential maximum cross-pollination. This maximum cross-pollination rate was 56.1%. A three-year field trial was also conducted to study the cross-pollination rates in terms of distance and orientation to an herbicide-resistant pollen source. Under field conditions, cross-pollination rates varied from 5.5% to 11.6% in plants adjacent to the pollen source and decreased with increasing distances (1.5 to 8.9% at 15 m distance and up to 4.1% at 25 m in the downwind direction). Environmental conditions influenced the cross-pollination both under greenhouse and field conditions. Data were fit to an exponential decay model to predict gene flow at increasing distances. This model predicted an average gene flow of 7.1% when the pollen donor and recipient plants were at 0 m distance from each other. Pollen-mediated gene flow declined by 50% at 16.7 m from the pollen source, yet under downwind conditions gene flow of 5.2% was predicted at 25 m, the farthest distance studied. Knowledge of cross-pollination rates will be useful for assessing the spread of herbicide resistance genes in L. rigidum and in developing appropriate strategies for its mitigation.
BACKGROUND
Corn poppy ( Papaver rhoeas ) is the most damaging broadleaf weed in France. Massively parallel amplicon sequencing was used to investigate the prevalence, mode of evolution and spread of resistance‐endowing ALS alleles in 422 populations randomly sampled throughout poppy's range in France. Bioassays were used to detect resistance to the synthetic auxin 2,4‐D in 43 of these populations.
RESULTS
A total of 21,100 plants were analysed and 24 mutant ALS alleles carrying an amino‐acid substitution involved or potentially involved in resistance were identified. The vast majority (97.6%) of the substitutions occurred at codon Pro197, where all six possible single‐nucleotide non‐synonymous substitutions plus four double‐nucleotide substitutions were identified. Changes observed in the enzymatic properties of the mutant ALS isoforms could not explain the differences in prevalence among the corresponding alleles. Sequence read analysis showed that mutant ALS alleles had multiple, independent evolutionary origins, and could have evolved several times independently within an area of a few kilometres. Finally, 2,4‐D resistance was associated with mutant ALS alleles in individual plants in one third of the populations assayed.
CONCLUSION
The intricate geographical mosaic of mutant ALS alleles observed is the likely result of the combination of huge population sizes, multiple independent mutation events and human‐mediated spread of resistance. Our work highlights the ability of poppy populations and individual plants to accumulate different ALS alleles and as yet unknown mechanisms conferring resistance to synthetic auxins. This does not bode well for the continued use of chemical herbicides to control poppy.
This article is protected by copyright. All rights reserved.
The development of resistance in Alopecurus myosuroides populations to different herbicide active ingredients in Europe exacerbates efforts toward its chemical control. In Europe, cinmethylin provides an additional mode of action for the control of A. myosuroides . The objective of this study was to evaluate three resistance weed management (RWM) strategies, including cinmethylin and other pre‐emergence herbicides, for the control of multiple herbicide–resistant A. myosuroides . The RWM strategies used in this study differed in the extent of preventive cultural practices (tillage, crop rotation, sowing date and stale seedbed). Two field trials were conducted at sites with ACCase‐ and ALS‐resistant A. myosuroides biotypes in Germany between 2017 and 2020. Cinmethylin was included in the herbicide regime for A. myosuroides control. The combination of initial inversion tillage, delayed sowing, crop rotation diversification, and stale seedbed reduced the density of A. myosuroides bup to 90% compared to a strategy with pre‐emergence herbicides used as main components in control. At both sites, the amount of viable A. myosuroides seeds in the soil seed bank was reduced by over 90% after a 3‐year trial period in plots with initial inversion tillage. Molecular analyses revealed that the omission of ACCase and ALS inhibitors did not reduce the proportion of resistant A. myosuroides biotypes. Long‐term control of resistant A. myosuroides must be based on a combination of cultural practices that reduce the soil seed bank and suppress the occurrence of A. myosuroides and the use of still‐effective active ingredients for preventing the renewed entry of seeds into the soil.
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.
Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here we examine the potential for life history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp ® , the most commonly used herbicide worldwide. We find evidence for life history trade-offs associated with all three traits; highly resistant populations had lower germination rates, shorter roots and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.
Alopecurus myosuroides Huds. is one of the most problematic grass weeds in cereal production in Western Europe. This grass weed spread rapidly due to the repeated and intensive use of herbicides with the same mode of action and changes in arable cropping and tillage systems. Herbicide applications are the common agricultural practice for successful control of A. myosuroides due to its high flexibility and low cost. However, due to European and national restrictions and the growth of herbicide-resistant populations, farmers are forced to reduce herbicide use to minimize chemical impacts on the environment and food chain. As a holistic approach for reducing herbicide use, integrated weed management (IWM) is a diversification of the control strategy of A. myosuroides. In this thesis, several aspects of IWM were examined and combined to test for a successful A. myosuroides control strategy in winter cereals. Special attention was paid to cinmethylin, a pre-emergence herbicide with a new mode of action in winter cereals to control A. myosuroides. The first article comprised the development of an agar bioassay sensitivity test to determine sensitivity differences in A. myosuroides populations to pre-emergence herbicides containing flufenacet and the re-discovered substance cinmethylin. All of the tested populations did not show reduced sensitivity to cinmethylin, but differences in resistance factors were observed between the agar bioassay sensitivity test and the standard whole plant pot bioassay in the greenhouse. Nevertheless, it was possible for the most part to confirm the results for cinmethylin and flufenacet of the standardized greenhouse whole plant pot bioassay in the agar bioassay sensitivity tests and hence create a reliable, faster test system. The second article focused on cultural measures like cover crop mixtures, various stubble tillage methods and glyphosate treatments and their effect on total weed infestation in particular on A. mysouroides and volunteer wheat. Within two field experiments, the cover crop mixtures and the dual glyphosate application achieved a control efficacy of A. myosuroides of up to 100%, whereas stubble tillage and the single glyphosate treatment did not reduce A. myosuroides population significantly. The results demonstrated, that besides a double glyphosate application, well developed cover crop mixtures have a great ability for weed control, even for A. myosuroides. The third article also dealed with the combination of cultural measures (delayed seeding) and herbicide application and their influence on A. myosuroides control efficacy and yield response of winter wheat and triticale. Results indicate that cultural methods such as delayed seeding can reduce A. myosuroides populations up to 75%, although to achieve control efficacy of > 95%, supplementary herbicides should be used. In the fourth article, a two-year experiment on two experimental sites was set up with a special focus on stubble tillage methods, glyphosate application and the application of the pre-emergence herbicide cinmethylin in two rates. Control efficiencies of 99-100% were achieved by ploughing, double glyphosate application or via false seedbed preparation, each in combination with a cinmethylin application. In the last article, over a period of three years the new pre-emergence herbicide cinmethylin was tested in combination with stubble treatments and delayed drilling of winter annual cereals in winter wheat and winter triticale in Southwestern Germany. Cinmethylin controlled 58-99% of A. myosuroides plants until 120 days after sowing. Additive and synergistic effects of cinmethylin and delayed drilling were found for all studies. In this study, the focus was set on monitoring, cultural and direct weed control methods. Considering especially A. myosuroides, a diverse control strategy needs to be implemented to ensure a sustainable and reduced herbicide use, high control levels, minimized crop damage, safeguarded grain yields and reduced risk of resistance development. However, IWM measures imply increased system complexity, which may make their adoption by farmers difficult. Nevertheless, the results show that cinmethylin can be successfully used for weed control systems in combination with different stubble tillage methods, glyphosate application, delayed seeding, or herbicide sequences and mixtures, making it a valuable tool in integrated weed and resistance management strategies with its novel and unique mode of action.
Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of common waterhemp ( Amaranthus tuberculatus ), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size (N e ) estimate of 8x10 ⁷ . We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median allele age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.
Despite the considerable research efforts invested over the years to measure the fitness costs of herbicide resistance, these have rarely been used to inform a predictive theory about the fate of resistance once the herbicide is discontinued. One reason for this may be the reductive focus on relative fitness of two genotypes as a single measure of differential performance. Although the extent of variation in relative fitness between resistant and susceptible plants has not been assessed consistently, we know enough about plant physiology and ecology not to reduce it to a single fixed value. Research must therefore consider carefully the relevance of the experimental environment, the life stage and the choice of metric when measuring fitness-related traits. The reason most often given for measuring the cost of resistance, prediction of the impacts of management options on population dynamics, cannot be addressed using arbitrary components of fitness or a fixed value of relative fitness. To inform management options, the measurement of traits that capture the relevant processes and the main causes of their variation are required. With an emphasis on the benefit of field experiments measured over multiple time points and seasons, we highlight examples of studies that have made significant advances in this direction.
The evolution of herbicide resistance is an important topic in plant protection and agricultural practice. Safeners are commonly used in herbicides to protect crops against herbicidal damage. Although no effect on the weed control is expected, it has been theorized that the rate of evolution of non-target site resistance (NTSR) in weeds in cereals may be enhanced by use of herbicide products containing safeners. One of the most important safeners in cereals is mefenpyr-diethyl. Therefore, the possible influence of mefenpyr on herbicide resistance was studied in cooperative trials between Bayer CropScience (BCS, F-Höchst) and FH Bingen. The trials tested in parallel different herbicide resistant black-grass (Alopecurus myosuroides (Huds.)) biotypes under greenhouse conditions. The biotypes where chosen due to known NTSR against Atlantis WG® (4 highly resistant and 5 moderately resistant) as well as two susceptible biotypes. The populations were treated with the following three herbicide/safener regimes in six concentrations adjusted according to the anticipated biotype resistance levels. (1) mesosulfuron + iodosulfuron + without safener formulation, (2) mesosulfuron + iodosulfuron + constant mefenpyr concentration (45g/ha), (3) mesosulfuron + iodosulfuron + varying mefenpyr concentrations (ratio 5:1:15). The treatments were applied in post-emergence based on mesosulfuron to iodosulfuron ratios in Atlantis WG® (5:1). The trials were assessed visually (% effect) and by fresh weight. Dose-response curves were performed and ED50 values for each treatment and biotype were calculated. Results showed a varying effect of safeners which was in the most cases negligible. Depending on the biotypes mostly no impact on the safener was found for herbicide resistance. In conclusion, the trials from Bingen and F-Höchst gave evidence, that there is no significant and consistent influence of the safener mefenpyr on evolution of NTSR black-grass.
This chapter focuses on one weed species, Alopecurus myosuroides, and on resistance to two herbicide groups acting on two modes of action: on acetolactate-synthase (ALS; also called acetohydroxyacid synthase (AHAS)) and on acetyl-CoA-carboxylase (ACCase). The mechanisms of resistance to these herbicides can be both target site resistance mechanisms (TSR) and non-target site resistance mechanisms (NTSR). The chapter reviews a particular case study project that was started in southern Germany with the aim of following the development of herbicide resistance of Alopecurus myosuroides in space and time under similar climatic and agricultural conditions but on fields with different field histories and different agronomic practices used by the respective farmers. The actual situation in the field is much more complicated with different crop management tools involving mechanical weed control, crop rotation, multiple treatments at different weed stages, stubble treatments, herbicide mixtures, and more.
Total pollen production per inflorescence was studied in the most important species of the Poaceae family in the city of Córdoba in order to further our knowledge of the partial contribution of each species of this family to the total amount of pollen released into the atmosphere.The contribution of grasses in a given area was estimated by counting the number of inflorescences in an area of one square meter. Four different representative areas of the city were selected. The number of pollen grains per anther and flowers per inflorescence was also estimated in order to obtain total pollen production per inflorescence.Pollen production per inflorescence ranged from 14,500 to more than 22,000,000 pollen grains, the amount being clearly higher in the perennial species. Pollen production per square meter was higher in the mountains near the city and lower in areas of abandoned crops.Only a few species are responsible for the majority of pollen produced. A phenological study is necessary in order to determine the temporal distribution of this pollen production and subsequent shedding.
The damson–hop aphid, Phorodon humuli (Schrank), is a serious pest of hops in England. It is holocyclic (with obligatory sexual phase) and host alternating. From suction trap data, P. humuli aerial densities are known to be greatest in the main hop growing regions of Herefordshire and Kent (mid-west and south-east England, respectively), some 260 km apart. The aphid is now resistant to several insecticides. This is in part conferred by elevated carboxylesterase activity, ranging from low in susceptible to high in very resistant strains. Enzyme markers, including carboxylesterases (EST-4 to -7), separated electrophoretically from individual insects, have been used to examine the degree of genetic heterogeneity among P. humuli sub-populations on both its hosts – Prunus spp. (primary overwintering host) and hops, Humulus lupulus (secondary summer host). The esterase data revealed heterogeneity among subpopulations collected from wild, unsprayed hosts in regions less than 30 km in area, with a higher mean frequency of elevated esterase variants in the commercial hop growing regions of Herefordshire and Kent, compared with samples from a non-commercial region around Rothamsted. Esterase distributions remained similar over consecutive years. Similarly, allele and genotype frequencies for another enzyme (6-phosphogluconate dehydrogenase, 6-PGD) were also heterogeneous among subpopulations sampled at less than 30 km apart (especially from Prunus) in each of the three regions surveyed, whilst allele and genotype frequencies sometimes remained stable over a number of summers. In addition, 6-PGD genotype frequencies were mostly congruent with Hardy-Weinberg expectations, even for parthenogenetically-reproducing aphids colonizing hops. These data suggest that the 6-PGD alleles tested are selectively neutral; that gene flow (=migration) is restricted between aphid populations, even within a single region (≤ 30 km) and, that the autumn migration from hops to Prunus is probably of shorter range (perhaps less than 20 km) compared with the spring migration from Prunus to hops.
Summary Weeds cause yield losses and reductions in crop quality. Prior to the introduction of selective herbicides, the drudgery of manual weeding forced farmers to adhere to a suit of weed management tactics by carefully combining crop rotation, appropriate tillage and fallow systems. The introduction of selective herbicides in the late 1940s and the constant flow of new herbicides in the succeeding decades provided farmers with a new tool, ‘the chemical hoe’, putting them in a position to consider weed control more independently of the crop production system than hitherto. The reliance on herbicides for weed control, however, resulted in shifts in the weed flora and the selection of herbicide-resistant biotypes. In the 1980s, the public concern about side-effects of herbicides on the environment and human health resulted in increasingly strict registration requirements and, in some countries, political initiatives to reduce the use of pesticides were launched. Today, the number of new herbicides being introduced has decreased significantly and integrated weed management has become the guiding concept. Farmers also have the option of growing herbicide-resistant crops where the biology of the crop has been adapted to tolerate herbicides considered safe to humans and environmentally benign. This paper discusses some of the recent developments in herbicide discovery, technology and fate, and sketches important future developments.
Blackgrass (Alopecurus myosuroides Huds.) seed dispersal from single mother-plants was studied in two experiments. For the first experiment, eight blackgrass plants of different heights and number of ears were produced in a greenhouse with the help of different in sowing densities and nitrogen nutrition levels. At the beginning of seed shedding, the plants were placed outside, and seeds were gathered daily. Daily seed dispersal was analysed by fitting a Weibull equation to the number of seeds as a function of distance to the mother-plant. The second experiment was carried out in a field comprising winter barley and spring barley plots as well as bare soil. In each of these three parts, two isolated blackgrass plants were selected and seeds gathered with the help of small pots located along and across the crop rows at growing distances from the mother-plants. For both experiments, total seed dispersal was analysed by fitting a sum of two Weibull equations and analysing the estimated parameters as a function of blackgrass characteristics (plant height, number of ears per plants), seed characteristics (weight, presence of caryopsis, germination ability), crop cover (winter barley, spring barley, no crop) and direction (along or across crop rows). The dispersal equations were then introduced into a weed demography model, and blackgrass spread in time and in space was simulated for a field cultivated with different crops.
Formulae are given for estimators for the parameters F, θ, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.
Pollen is an important vector of gene flow in plants, particularly for outcrossing species like tall fescue. Several aspects of pollination biology were investigated using pollen from transgenic and nontransgenic plants of tall fescue (Festuca arundinacea Schreb.), the most important forage species worldwide of the Festuca genus. To effectively assess in vitro pollen viability in tall fescue, an optimized germination medium (0.8 mol/L sucrose, 1.28 mmol/L boric acid and 1.27 mmol/L calcium nitrate) was developed. Treatment with relatively high temperatures (36° and 40°C) and high doses of UV-B irradiation (900-1500 μW/cm(2)) reduced pollen viability, while relative humidity did not significantly influence pollen viability. Viability of pollen from transgenic progenies (T1 and T2) was similar to that from seed-derived control plants. Pollen from primary transgenics (T0) and primary regenerants (R0) had various levels of viability. Hand pollination using the primary regenerants and transgenics revealed that no seed set could be obtained when pollen viability was lower than 5%. Pollen from transgenic progenies and nontransgenic control plants could survive up to 22 h under controlled conditions in growth chamber. However, under sunny atmospheric conditions, viability of transgenic and nontransgenic pollen reduced to 5% in 30 min, with a complete loss of viability in 90 min. Under cloudy atmospheric conditions, pollen remained viable up to 240 min, with about 5% viability after 150 min. This report is the first on pollen viability and longevity in transgenic forage grasses and could be useful for risk assessment of transgenic plants.
GeneSys models the effects of regional cropping systems on gene flow between cropped and volunteer rape plants. Its sensitivity to field patterns and cropping system input variables was analysed using Monte Carlo simulations of which the output was analysed by regression trees and linear regressions. The studied simulated output variable was the harvest contamination of conventional crops by genetically modified seeds. The study showed that field characteristics (areas, shapes, distances and orientation) have little effect compared with cropping systems. Gene flow increased with the area of the pollen- and seed-producing field and decreased with the area of the gene-receiving field; it increased for elongated vs. square fields and decreased with the distance between fields. The sensitivity analysis identified the distance and time during which cropping systems influence harvest contamination in various field plants. The harvest purity of a cluster of fields was influenced by the cropping history of the fields located less than 200 to 400 m around the cluster, and of three past years in addition to the ongoing analysed year for major variables such as crop succession or sowing date. The analysis of these major variables pointed to strategies for reducing gene flow, such as increasing the time between successive rape varieties; avoiding high-risk crops such as genetically modified (GM) rape and set-aside in the neighbouring fields for the year preceding the cultivation of a non-GM crop as well as the year during which the non-GM rape is grown; delaying the sowing of non-GM rape.
We examine the power of different exact tests of differentiation for diploid populations. Since there is not necessarily random mating within populations, the appropriate hypothesis to construct exact tests is that of independent sampling of genotypes. There are two categories of tests, FST-estimator tests and goodness of fit tests. In this latter category, we distinguish "allelic statistics", which account for the nature of alleles within genotypes, from "genotypic statistics" that do not. We show that the power of FST-estimator tests and of allelic goodness of fit tests are similar when sampling is balanced, and higher than the power of genotypic goodness of fit tests. When sampling is unbalanced, the most powerful tests are shown to belong to the allelic goodness of fit group.
Due to the surge in interest in using single nucleotide polymorphisms (SNPs) for genotyping a facile and affordable method for this is an absolute necessity. Here we introduce a procedure that combines an easily automatable single tube sample preparation with an efficient high throughput mass spectrometric analysis technique. Known point mutations or single nucleotide polymorphisms are easily analysed by this procedure. It starts with PCR amplification of a short stretch of genomic DNA, for example an exon of a gene containing a SNP. By shrimp alkaline phosphatase digest residual dNTPs are destroyed. Allele-specific products are generated using a special primer, a conditioned set of alpha-S-dNTPs and alpha-S-ddNTPs and a fresh DNA polymerase in a primer extension reaction. Unmodified DNA is removed by 5'-phospho-diesterase digestion and the modified products are alkylated to increase the detection sensitivity in the mass spectrometric analysis. All steps of the preparation are simple additions of solutions and incubations. The procedure operates at the lowest practical sample volumes and in contrast to other genotyping protocols with mass spectrometric detection requires no purification. This reduces the cost and makes it easy to implement. Here it is demonstrated in a version using positive ion detection on described mutations in exon 17 of the amyloid precursor protein gene and in a version using negative ion detection on three SNPs of the granulocyte-macrophage colony stimulating factor gene. Preparation and analysis of SNPs is shown separately and simultaneously, thus demonstrating the multiplexibility of this genotyping procedure. The preparation protocol for genotyping is adapted to the conditions used for the SNP discovery method by denaturing HPLC, thus demonstrating a facile link between protocols for SNP discovery and SNP genotyping. Results corresponded unanimously with the control sequencing. The procedure is useful for high throughput genotyping as it is required for gene identification and pharmacogenomics where large numbers of DNA samples have to be analysed. We have named this procedure the 'GOOD Assay' for SNP analysis.
The resistance of gastro-intestinal nematodes of small ruminants (sheep and goat) to benzimidazole anthelmintic drugs seems to be linked primarily to a single mutation in the isotype 1 beta-tubulin gene. This study was carried out to investigate the origin and diversity of benzimidazole-resistance alleles in trichostrongylid nematodes. We sequenced a 550 bp fragment of the isotype 1 beta-tubulin gene from several benzimidazole-resistant Teladorsagia circumcincta populations isolated from dairy goat farms in the central and south-western France. We also sequenced the same beta-tubulin fragment from Trichostrongylus colubriformis and Haemonchus contortus populations in south-western France. We found eight benzimidazole-resistance alleles in all T. circumcincta populations studied, six in H. contortus populations, and only one in T. colubriformis populations. In most cases, only one benzimidazole-resistance allele was present in T. circumcincta and H. contortus populations, but two alleles were found in a fewer number of them. Some T. circumcincta populations shared the same benzimidazole-resistance allele whereas some others had a specific benzimidazole-resistance allele. Similar findings were obtained for H. contortus. As no parasites are introduced once the flock of dairy goat farms has been constituted, these data indicate for the three studied species that rare pre-existing benzimidazole-resistance alleles already present before the isolation of populations had been selected. On the other hand, the fact that some benzimidazole-resistance alleles were specific to one population of T. circumcincta or H. contortus, seems to be in agreement with the hypothesis of the selection of spontaneous mutations. Thus, the origin of benzimidazole-resistance alleles in trichostrongylid nematodes seems to involve primarily the selection of rare alleles and possibly of spontaneous mutations.
A 3,300-bp DNA fragment encoding the carboxyl-transferase domain of the multidomain, chloroplastic acetyl-coenzyme A carboxylase (ACCase) was sequenced in aryloxyphenoxypropionate (APP)-resistant and -sensitive Alopecurus myosuroides (Huds.). No resistant plant contained an Ile-1,781-Leu substitution, previously shown to confer resistance to APPs and cyclohexanediones (CHDs). Instead, an Ile-2,041-Asn substitution was found in resistant plants. Phylogenetic analysis of the sequences revealed that Asn-2,041 ACCase alleles derived from several distinct origins. Allele-specific polymerase chain reaction associated the presence of Asn-2,041 with seedling resistance to APPs but not to CHDs. ACCase enzyme assays confirmed that Asn-2,041 ACCase activity was moderately resistant to CHDs but highly resistant to APPs. Thus, the Ile-2,041-Asn substitution, which is located outside a domain previously shown to control sensitivity to APPs and CHDs in wheat (Triticum aestivum), is a direct cause of resistance to APPs only. In known multidomain ACCases, the position corresponding to the Ile/Asn-2,041 residue in A. myosuroides is occupied by an Ile or a Val residue. In Lolium rigidum (Gaud.), we found Ile-Asn and Ile-Val substitutions. The Ile-Val change did not confer resistance to the APP clodinafop, whereas the Ile-Asn change did. The position and the particular substitution at this position are of importance for sensitivity to APPs.
In grasses, residues homologous to residues Ile-1,781 and Ile-2,041 in the carboxyl-transferase (CT) domain of the chloroplastic acetyl-coenzyme A (CoA) carboxylase (ACCase) from the grass weed black-grass (Alopecurus myosuroides [Huds.]) are critical determinants for sensitivity to two classes of ACCase inhibitors, aryloxyphenoxypropionates (APPs) and cyclohexanediones. Using natural mutants of black-grass, we demonstrated through a molecular, biological, and biochemical approach that residues Trp-2,027, Asp-2,078, and Gly-2,096 are also involved in sensitivity to ACCase inhibitors. In addition, residues Trp-2,027 and Asp-2,078 are very likely involved in CT activity. Using three-dimensional modeling, we found that the side chains of the five residues are adjacent, located at the surface of the inside of the cavity of the CT active site, in the vicinity of the binding site for APPs. Residues 1,781 and 2,078 are involved in sensitivity to both APPs and cyclohexanediones, whereas residues 2,027, 2,041, and 2,096 are involved in sensitivity to APPs only. This suggests that the binding sites for these two classes of compounds are overlapping, although distinct. Comparison of three-dimensional models for black-grass wild-type and mutant CTs and for CTs from organisms with contrasted sensitivity to ACCase inhibitors suggested that inhibitors fitting into the cavity of the CT active site of the chloroplastic ACCase from grasses to reach their active sites may be tight. The three-dimensional shape of this cavity is thus likely of high importance for the efficacy of ACCase inhibitors.
*INRA Laboratoire de Malherbologie BP 86510 21065 Dijon cedex (FRA) Diffusion du document : INRA Laboratoire de Malherbologie BP 86510 21065 Dijon cedex (FRA) Diplôme : Dr. d'Université
The nature and occurrence of herbicide resistance in wild oat in annual crops grown in the Grassland and Parkland regions of Saskatchewan were determined in a systematic survey of fields in two townships in 1997. The survey found that over one-half of fields in both townships had populations resistant to Group 1 [acetyl-CoA carboxylase (ACCase) inhibitors], Group 2 [acetolactate synthase (ALS) inhibitors], and/or Group 8 (e.g., triallate, difenzoquat) herbicides. Forty-three percent of fields in the Grassland township and 48% of fields in the Parkland township had Group 1-resistant (HR) wild oat; 30 and 17% of fields in the Grassland and Parkland township, respectively, had populations exhibiting Group 2 resistance, whereas about 15% of fields in both townships had Group 8-HR wild oat. Single- (Groups 1, 2, or 8) and multiplegroup resistance (1, 2; 1, 8; 2, 8; 1, 2, 8) were exhibited in populations in fields in both townships. Frequency of occurrence of resistance was not generally affected by farm size. The nature of resistance in wild oat populations is more diverse, differences in distribution and abundance of HR wild oat biotypes between Grassland and Parkland regions are generally less apparent, and occurrence of resistance is more prevalent than documented previously.
Surveys were conducted across the northern Great Plains of Canada in 1996 and 1997 to determine the nature and occurrence of herbicide-resistant (HR) biotypes of wild oat (Avena fatua). The surveys indicated that resistance to acetyl-CoA carboxylase (ACCase) inhibitors (Group 1) occurred most frequently relative to other herbicide groups. Group 1-HR wild oat occurred in over one-half of fields surveyed in each of the three prairie provinces. Of particular concern was the relatively high incidence of multiple-group resistance in wild oat in Saskatchewan and Manitoba. In Saskatchewan, 18% of Group 1-HR populations were also resistant to acetolactate synthase inhibitors (imidazolinones), even though these herbicides were not frequently used. In Manitoba, 27% of fields surveyed had wild oat resistant to herbicides from more than one group. Four populations were resistant to all herbicides registered for use in wheat (Triticum aestivum). Depending on the nature of resistance in wild oat, alternative herbicides available for their control may substantially increase costs to the grower. The cost to growers of managing HR wild oat in Saskatchewan and Manitoba using alternative herbicides is estimated at over $4 million annually. For some HR biotypes, alternative herbicides either are not available or all have the same site of action, which restricts crop or herbicide rotation options and threatens the future sustainability of small-grain annual cropping systems where these infestations occur.
Sethoxydim-resistant biotypes of Setaria faberi Herrm. (giant foxtail) and Setaria viridis L. Beauv. (green foxtail) were identified in Iowa, USA in 1994 and Manitoba, Canada in 1991, respectively. Sethoxydim and related herbicides inhibit acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) in sensitive grass species. ACCase from susceptible biotypes of the two species was very sensitive to sethoxydim and a selection of other ACCase inhibitors; including clethodim, fenoxaprop and quizalofop, with I50 values of 0.3-6.5 μM and 2.1-7.7 μM for S. faberi and S. viridis, respectively. In contrast, ACCase from the resistant biotypes was very resistant to sethoxydim (I50 of 1250 and 3260 μM for S. faberi and S. viridis, respectively) and resistant, although to a lesser extent, to the other herbicides tested. The results indicate that resistance to ACCase inhibitors in these biotypes is due to an alteration in the target enzyme, ACCase, that confers a very high level of resistance to sethoxydim and lower levels of resistance to other ACCase-inhibiting herbicides.
Due to the surge in interest in using single nucleotide polymorphisms (SNPs) for genotyping a facile and affordable method for this is an absolute necessity. Here we introduce a procedure that combines an easily automatable single tube sample preparation with an efficient high throughput mass spectrometric analysis technique. Known point mutations or single nucleotide polymorphisms are easily analysed by this procedure. It starts with PCR amplification of a short stretch of genomic DNA, for example an exon of a gene containing a SNP. By shrimp alkaline phosphatase digest residual dNTPs are destroyed. Allele-specific products are generated using a special primer, a conditioned set of α-S-dNTPs and α-S-ddNTPs and a fresh DNA polymerase in a primer extension reaction. Unmodified DNA is removed by 5′-phosphodiesterase digestion and the modified products are alkylated to increase the detection sensitivity in the mass spectrometric analysis. All steps of the preparation are simple additions of solutions and incubations. The procedure operates at the lowest practical sample volumes and in contrast to other genotyping protocols with mass spectrometric detection requires no purification. This reduces the cost and makes it easy to implement. Here it is demonstrated in a version using positive ion detection on described mutations in exon 17 of the amyloid precursor protein gene and in a version using negative ion detection on three SNPs of the granulocyte-macrophage colony stimulating factor gene. Preparation and analysis of SNPs is shown separately and simultaneously, thus demonstrating the multiplexibility of this genotyping procedure. The preparation protocol for genotyping is adapted to the conditions used for the SNP discovery method by denaturing HPLC, thus demonstrating a facile link between protocols for SNP discovery and SNP genotyping. Results corresponded unanimously with the control sequencing. The procedure is useful for high throughput genotyping as it is required for gene identification and pharmacogenomics where large numbers of DNA samples have to be analysed. We have named this procedure the ‘GOOD Assay’ for SNP analysis.
Herbicides targeting grass plastidic acetyl coenzyme A carboxylase (ACC) are effective
selective graminicides. Their intensive use worldwide has selected for resistance genes
in a number of grass weed species. Biochemistry and molecular biology have been
the means of determining the herbicidal activity and selectivity toward crop plants
of ACC-inhibiting herbicides. In recent years, elucidation of the tridimensional structure
of ACC and identification of five amino acid residues within the ACC carboxyl
transferase domain that are critical determinants for herbicide sensitivity shed light
on the basis of ACC-based resistance to herbicides. However, metabolism-based resistance
to ACC-inhibiting herbicides is much less well known, although this type
of resistance seems to be widespread. A number of genes thus endow resistance to
ACC-inhibiting herbicides, with the possibility for various resistance genes that confer
dominant resistance at the herbicide field rate to accumulate within a single weed
population or plant. This, together with a poor knowledge of the genetic parameters
driving resistance, renders the evolution of resistance to ACC-inhibiting herbicides
unpredictable. Future research should consider developing tactics to slow the spread
of resistance. For this purpose, it is crucial that our understanding of metabolismbased
resistance improves rapidly because this mechanism is complex and can confer
resistance to herbicides with different target sites.
The tremendous advances in electronic data processing are likely to result in revolutionary changes in the theories and practices of taxonomy. The process of classification is being removed from speculations regarding the origin of the taxa being classified. A natural classification is one whose taxa share the largest number of properties and which is most useful for a wide range of purposes. The principles of numerical taxonomy are stated briefly and illustrated by means of diagrammatic examples. The relative roles of the taxonomist and computer are discussed and estimates given of computer time and costs involved in numerical taxonomic work. The numerical taxonomic work done in botany so far is discussed and the paper concludes with a brief mention of several problems of numerical taxonomy with regard to botanical work. These are: scarcity of characters, correlations between cytogenetic work and phenetic similarities, and problems raised by hybridization.
A survey conducted across agricultural ecoregions of Saskatchewan in 1996 revealed that wild oat (Avena fatua) populations resistant to acetyl-CoA carboxylase (ACCase) inhibitors were present in approximately 10% of Saskatchewan fields (2.4 million ha). In the Aspen Parkland and Boreal Transition ecoregions, this increased to 17%. The objective of this study was to determine if agronomic practices promoted or delayed resistance and to assess producer awareness of herbicide resistance. Weed resistance and management questionnaire data from the 1996 resistance survey and management questionnaire data from the 1995 Saskatchewan weed survey were submitted to multiway frequency analysis. The frequency of occurrence of herbicide-resistant wild oat was related directly to ACCase inhibitor use. Resistance to cyclohexanedione (CHD) herbicides was not related to CHD use but to frequency of ACCase inhibitor use (i.e., CHD + aryloxyphenoxypropanoate [AOPP]), suggesting that the pressure imposed by AOPPs contributed to the selection of CHD resistance in wild oat. ACCase inhibitor use was more extensive in the Aspen Parkland and Boreal Transition ecoregions than in the Mixed and Moist Mixed Grassland ecoregions, Crop rotations were not conducive to rotation of herbicides with different sites of action, Frequency of ACCase inhibitor use increased with frequency of annual crops, in spite of the inclusion of cereal and dicot crops in the rotation. Producers utilizing conservation tillage practices in the Grassland ecoregions used proportionally more ACCase inhibitors than those using conventional tillage practices. This increase in ACCase use in conservation tillage systems did not result in an increased incidence of wild oat populations resistant to ACCase inhibitors. Producers reporting troublesome wild oat populations tended to have proportionally more ACCase resistant wild oat. Producers who reported practicing weed sanitation were less likely to have resistant wild oat than those who were less careful. Increased awareness and implementation of management practices that will reduce the dependency on ACCase herbicides are required to better enable producers to prevent, delay, or manage herbicide-resistant wild oat populations.
Primers were designed to amplify two regions involved in sensitivity to herbicides inhibiting the plastidic acetyl-CoA carboxylase (ACCase) from grasses (Poaceae). The first primer pair amplified a 551-bp amplicon containing a variable Ile/Leu codon at position 1781 in Alopecurus myosuroides sequence. The second primer pair amplified a 406-bp amplicon containing four variable codons (Trp/Cys, Ile/Asn, Asp/Gly, Gly/Ala) at positions 2027, 2041, 2078 and 2096, respectively, in A. myosuroides sequence. Both primer pairs amplified the targeted fragments from genes encoding plastidic ACCases, but not from the very similar genes encoding cytosolic ACCases. Clear DNA sequences were obtained from fresh or dried plant material from the field, and from 29 various grass species. Sequences revealed that the gene encoding plastidic ACCase in Poa annua and Festuca rubra contained a Leu1781 codon, in agreement with both species being inherently tolerant to herbicides inhibiting ACCase. Sequencing confirmed the hybrid origin of P. annua. Compared with ACCase enzyme assay, polymerase chain reaction is faster, can be performed from a single plant and suppresses the need for radioactive experiments. It can be completed with basic molecular biology laboratory equipment. It is the tool of choice for diagnosing resistance caused by alteration(s) of the plastidic ACCase.
Regionalization is the primary classification problem in geography, although other typologies are sometimes demanded by specific research endeavors. Groupings of area units can produce either contiguous or fragmented patterns. Dis-contiguous regionalizations may have the advantage of placing truly alike areal units in the same category and are obviously necessary when the similarity of distant places is sought. The same number of contiguous regions, on the other hand, will most likely produce a more regular map pattern, thereby facilitating the transferral of the printed map into a more coherent and more lasting mental image.' Furthermore, many problems, particularly those partitioning space for administrative purposes, demand contiguity. Although some within-group homo-geneity is often lost by imposing contiguity, this is a difficulty only for situations with relatively low spatial consistency.a This loss of homogeneity may well be offset by the perceptual advantage of simplicity. Previous quantitative approaches to regional clustering have largely achieved contiguity by prohibiting linkages from occurring unless the two places abut. This contiguity restriction has been employed most often with hierarchical grouping procedures in which the clustering of N places proceeds through N-1 levels of classification to the ultimate aggregation of all units into a single group? At * The author is grateful to the Research Foundation of the State University of New York for financial support and to Michael Dobson, Peter Gould, and Anthony Williams for helpful suggestions. 1 For a discussion of the perceptual advantages of regular map patterns, see Monmonier [PI. 2 Spence [I21 discusses this problem and gives an example in which the loss of homogeneity for M regions of N counties decreases as Af approaches both 1 and N. 8Two of the earliest users of this approach were Ray and Berry [ I l l. Mark S. Monmonier is associate professor of geography at Syracuse University.
The process of evolution of resistance to acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides was investigated in four distinct patches of Alopecurus myosuroides Huds. (black-grass) that occur within adjacent fields on a cereal farm in Nottinghamshire, UK. In one field, there was a `main' patch containing 96% resistant plants and two `satellite' patches containing ≈2.9% and 4.4% resistant plants, and in an adjacent field another patch contained 25% resistant plants. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction (PCR) was used to analyse variation at 30 genetic loci in at least 20 resistant and 20 sensitive individual plants from each patch, from additional resistant populations from Essex and Lincolnshire, and from a sensitive reference population. Banding patterns were found to be highly repeatable. Each patch contained a high level of genetic diversity, regardless of its resistance status, and there was evidence for genetic differences between the patches (Gst = 0.14, Nei's distances up to 0.26). There was no evidence that resistance had spread from the `main' patch to the others, as resistant and sensitive plants in the same patch were more closely related on average than were resistant plants from neighbouring patches. The most likely explanations of this distribution, and their implications, are discussed.
1 Long‐distance dispersal events are biologically very important for plants because they affect colonization probabilities, the probabilities of population persistence in a fragmented habitat, and metapopulation structure. They are, however, very difficult to investigate because of their low frequency. We reviewed the use of molecular markers in the population genetics approach to studying dispersal. With these methods the consequences of long‐distance dispersal are studied, rather than the frequency of the dispersal events themselves.
2 Molecular markers vary, displaying different amounts of variation and different modes of inheritance: they may be either dominant or codominant, and may or may not be subjected to genetic recombination. Use of markers has inspired the development of maximum likelihood techniques that take the evolutionary history of alleles into account while estimating gene flow.
3 Inferring seed dispersal rates from indirect measurements of gene flow involves three steps: (i) quantifying genetic differentiation among populations and using this to estimate the rate of gene flow; (ii) producing a genetic dispersal curve by regressing geographical distance among populations against the amount of gene flow; and (iii) separating seed‐mediated from pollen‐mediated gene flow, by comparing differentiation in nuclear vs. cytoplasmic molecular markers. In this way, potentially very low levels of gene flow can be detected.
4 The indirect approach is based on a number of assumptions. The validity of each assumption should be assessed by independent methods or the estimates of gene flow and dispersal should be mainly used in a comparative context. In metapopulations, with frequent extinction and colonization, the relationship between genetic differentiation and gene flow is not straightforward, and other methods should be used.
5 Highly variable molecular markers, especially microsatellites, have facilitated a direct genetic approach to measuring gene flow, based on parental analyses.
6 The population genetic approach provides different information about dispersal than ecological methods. Thus population genetic and ecological methods may supplement each other, and together lead to a better insight into the dispersal process than either of the methods on its own.
The number of origins of pesticide resistance-associated mutations is important not only to our understanding of the evolution
of resistance but also in modeling its spread. Previous studies of amplified esterase genes in a highly dispersive Culex mosquito have suggested that insecticide resistance-associated mutations (specifically a single-gene duplication event) can
occur a single time and then spread throughout global populations. In order to provide data for resistance-associated point
mutations, which are more typical of pesticide mechanisms as a whole, we studied the number of independent origins of cyclodiene
insecticide resistance in the red flour beetle Tribolium castaneum. Target-site insensitivity to cyclodienes is conferred by single point mutations in the gene Resistance to dieldrin (Rdl), which codes for a subunit of a γ-aminobutyric acid (GABA) receptor. These point mutations are associated with replacements
of alanine 302 which render the receptor insensitive to block by the insecticide. We collected 141 strains of Tribolium worldwide and screened them for resistance. Twenty-four strains contained resistant individuals. After homozygosing 23 of
these resistance alleles we derived a nucleotide sequence phylogeny of the resistant strains from a 694-bp section of Rdl, encompassing exon 7 (which contains the resistance-associated mutation) and part of a flanking intron. The phylogeny also
included six susceptible alleles chosen at random from a range of geographical locations. Resistance alleles fell into six
clades and three clades contained both resistant and susceptible alleles. Although statistical analysis provided support at
only the 5–6% level, the pattern of variation in resistance alleles is more readily explained by multiple independent origins
of resistance than by spread of a single resistance-associated mutation. For example, two resistance alleles differed from
two susceptible alleles only by the resistance-associated mutation itself, suggesting that they form the susceptible ancestors
and that resistance arose independently in several susceptible backgrounds. This suggests that in Tribolium Rdl, de novo mutations for resistance have arisen independently in several populations. Identical alleles were found in geographically distant regions as well, also
implying that some Rdl alleles have been exported in stored grain. These differences from the Culex study may stem both from differences in the population genetics of Tribolium versus that of mosquitoes and differences in mutation rates associated with point mutations versus gene duplication events.
The Tribolium data therefore suggest that multiple origins of insecticide resistance (associated with specific point mutations) may be
more common than the spread of single events. These findings have implications for the way in which we model the evolution
and spread of insecticide resistance genes and also suggest that parallel adaptive substitutions may not be uncommon in phyletic
evolution.
Observations were made on the effects of different levels of plant density and nitrogen nutrition on the development and seed production of a weed (Alopecurus myosuroides Hudson). Experiments were conducted in two greenhouses with one plant per pot in order to avoid competition for nitrogen absorption. The density effect was studied by increasing the number of pots per unit surface. The results indicated that the leaf and tiller appearance rates were modified by nitrogen availability on plant density. The lack of nitrogen and higher plant density increased the leaf and tiller appearance rate. Growth and seed production was strongly influenced by the plant density, and the increased nitrogen availability at a given density did not modify the values of growth parameters. Some parameters as flowering time or seed viability were not modified in our experiment conditions. Possibilities of using these results in cropping systems to improve the control of A. myosuroides are discussed.
The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more
accessible to biologists. This online resource, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html/gkd115_gml.html,
is intended to serve as a searchable, up-to-date, centralized jumping-off point to individual Web sites. An emphasis has also
been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections,
or other innovative approaches.
Pollen dispersal and gene flow in the grass meadow fescue (Festuca pratensis Huds.) were studied using two populations which were homozygous for different allozymes at the Gpi-2 locus. The populations were established in a concentric donor-acceptor field experiment. Gene flow was found mainly to be affected by the distance between the donor and acceptor plants. Analysing 21 132 acceptor plant progenies, gene flow was shown to decrease rapidly with distance to the donor field up to 75 m, and beyond this distance much more slowly. The ability of donor pollen to fertilize acceptor plants depended very much on the density of the acceptor plants. Pairs of acceptor plants produced more compatible pollen locally, and captured significantly less donor pollen than single-plants. Despite the higher seed production of acceptor plants planted in pairs, the absolute number of heterozygous seeds carrying the donor allele was always lower than for single-plants. Wind direction had only a slight effect upon the type of pollen captured. Because of pollen production within the two plant populations being continuous and overlapping, the time when anthesis occurred had little effect on gene flow between the populations. Vigorous and tall acceptor plants with many panicles, high seed yield and high 1000-seed weight were able to capture more donor pollen than shorter plants. The results may be used to assess the risk of gene flow and to develop strategies for monitoring the spread of transgenes from genetically modified grasses.
Examining genomic data for traces of selection provides a powerful tool for identifying genomic regions of functional importance. Many methods for identifying such regions have focused on conserved sites. However, positive selection may also be an indication of functional importance. This article provides a brief review of some of the statistical methods used to detect selection using DNA sequence data or other molecular data. Statistical tests based on allelic distributions or levels of variability often depend on strong assumptions regarding population demographics. In contrast, tests based on comparisons of the level of variability in nonsynonymous and synonymous sites can be constructed without demographic assumptions. Such tests appear to be useful for identifying specific regions or specific sites targeted by selection.
Chloroplastic acetyl CoA-carboxylase (ACCase) is the target of widely used, specific graminicide herbicides: cyclohexanediones (CHDs) and aryloxyphenoxypropionates (APPs). Resistance to these compounds is a worldwide, increasing problem. Population genetic studies aimed at understanding the dynamics of this situation and the diffusion of resistance genes within and between weed populations are challenging because biological assays are not adequate for this purpose, and because different mechanisms of resistance confer a similar resistance phenotype. Molecular markers for specifically detecting resistance genes are therefore urgently needed to conduct such studies. For this purpose, we cloned and sequenced the whole gene encoding chloroplastic ACCase in Alopecurus myosuroides Huds. (Black-grass). We identified two point mutations at nucleotide 5,341 that both cause an isoleucine-leucine substitution at position 1,781. Three bi-directional allele-specific PCR assays were developed, each detecting two distinct ACCase alleles with a single PCR reaction. The sensitivity of 1,190 seedlings of A. myosuroides to one CHD and one APP was determined. Genotyping revealed that, although resistant plants were only selected by APPs, the (1,781)Leu ACCase allele is a widespread, dominant gene of resistance to both APPs and CHDs. No other ACCase allele associated with resistance could be identified in this work. Useful applications of allele-specific PCR markers are population genetic studies as well as routine molecular diagnosis of herbicide resistance.
We have investigated the process of evolution of target-site-based resistance to herbicides inhibiting acetyl-CoA carboxylase (ACCase) in nine French populations of black-grass (Alopecurus myosuroides Huds). To date, two different ACCase resistant alleles are known. One contains an isoleucine-to-leucine substitution at position 1781, the second contains an isoleucine-to-asparagine substitution at position 2041. Using phylogenetic analysis of ACCase sequences, we showed that 1781Leu ACCase alleles evolved from four independent origins in the nine black-grass populations studied, while 2041Asn ACCase alleles evolved from six independent origins. No geographical structure of black-grass populations was revealed. This implies that these populations, although geographically distant, are, or have until recently been, connected by gene flows. Comparison of biological data obtained from herbicide sensitivity bioassay and molecular data showed that distinct resistance mechanisms often exist in a single black-grass population. Accumulation of different resistance mechanisms in a single plant was also demonstrated. We conclude that large-scale evolution of resistance to herbicides in black-grass is a complex phenomenon, resulting from the independent selection of various resistance mechanisms in local black-grass populations undergoing contrasted herbicide and agronomical selection pressures, and connected by gene flows whose parameters remain to be determined.
When sampling locations are known, the association between genetic and geographic distances can be tested by spatial autocorrelation or regression methods. These tests give some clues to the possible shape of the genetic landscape. Nevertheless, correlation analyses fail when attempting to identify where genetic barriers exist, namely, the areas where a given variable shows an abrupt rate of change. To this end, a computational geometry approach is more suitable because it provides the locations and the directions of barriers and because it can show where geographic patterns of two or more variables are similar. In this frame we have implemented Monmonier's (1973) maximum difference algorithm in a new software package to identify genetic barriers. To provide a more realistic representation of the barriers in a genetic landscape, we implemented in the software a significance test by means of bootstrap matrices analysis. As a result, the noise associated with genetic markers can be visualized on a geographic map and the areas where genetic barriers are more robust can be identified. Moreover, this multiple matrices approach can visualize the patterns of variation associated with different markers in the same overall picture. This improved Monmonier's method is highly reliable and can be applied to nongenetic data whenever sampling locations and a distance matrix between corresponding data are available.
Costs of resistance are predicted to reduce plant productivity in herbicide-resistant weeds. Lolium rigidum herbicide-susceptible individuals (S), individuals possessing cytochrome P450-based herbicide metabolism (P450) and multiple resistant individuals possessing a resistant ACCase and enhanced cytochrome P450 metabolism (ACCase/P450) were grown in the absence of mutual plant interaction to estimate plant growth traits. Both P450 and ACCase/P450 resistant phenotypes produced less above-ground biomass than the S phenotype during the vegetative stage. Reduced biomass production in the resistant phenotypes corresponded to a reduced relative growth rate and a lower net assimilation rate and rate of carbon fixation. There were no significant differences between the two resistant phenotypes, suggesting that costs of resistance are associated with P450 metabolism-based resistance. There were no differences in reproductive output among the three phenotypes, indicating that the cost of P450 resistance during vegetative growth is compensated during the production of reproductive structures. The P450-based herbicide metabolism is shown to be associated with physiological resistance costs, which may be manipulated by agronomic management to reduce the evolution of herbicide resistance.
Acetyl coenzyme A carboxylase (ACCase) is the target of highly effective herbicides. We investigated the nucleotide variability of the ACCase gene in a sample of 18 black-grass (Alopecurus myosuroides [Huds.]) populations to search for the signature of herbicide selection. Sequencing 3,396 bp encompassing ACCase herbicide-binding domain in 86 individuals revealed 92 polymorphisms, which formed 72 haplotypes. The ratio of nonsynonymous versus synonymous substitutions was very low, in agreement with ACCase being a vital metabolic enzyme. Within black grass, most nonsynonymous substitutions were related to resistance to ACCase-inhibiting herbicides. Differentiation between populations was strong, in contrast to expectations for an allogamous, annual plant. Significant H tests revealed recent hitchhiking events within populations. These results were consistent with recent and local positive selection. We propose that, although they have only been used since at most 15 black-grass generations, ACCase-inhibiting herbicides have exerted a positive selection targeting resistant haplotypes that has been strong enough to have a marked effect upon ACCase nucleotide diversity. A minimum-spanning network of nonrecombinant haplotypes revealed multiple, independent apparitions of resistance-associated mutations. This study provides the first evidence for the signature of ongoing, recent, pesticide selection upon variation at the gene encoding the targeted enzyme in natural plant populations.
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