Geographical variation in resistance to acetyl-coenzyme A carboxylase-inhibiting herbicides across the range of the arable weed Alopecurus myosuroides (black-grass)

Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil

An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.

ACCase gene mutations and P450-mediated metabolism contribute to cyhalofop-butyl resistance in Eleusine indica biotypes from direct-seeding paddy fields

Eleusine indica causes problems in direct-seeding rice fields across Jiangsu Province in China. Long-term application of chemical herbicides has led to the widespread evolution of resistance in E. indica. In this study, we surveyed the resistance level of cyhalofop-butyl (CyB) in 19 field-collected E. indica biotypes, and characterized its underlying resistance mechanisms. All 19 biotypes evolved moderate- to high-level resistance to CyB (from 5.8- to 171.1-fold). 18 biotypes had a target-site mechanism with Trp-1999-Ser, Trp-2027-Cys, or Asp-2078-Gly mutations, respectively. One biotype (JSSQ-1) was identified to have metabolic resistance, in which malathion pretreatment significantly reduced the CyB resistance, and cyhalofop acid was degraded 1.7- to 2.5-times faster in this biotype compared with a susceptible control. Furthermore, the JSSQ-1 biotype showed multiple resistance to acetyl-CoA carboxylase (ACCase) inhibitor metamifop (RI = 4.6) and fenoxaprop-p-ethyl (RI = 5.1), acetolactate synthase (ALS) inhibitor imazethapyr (RI = 4.1), and hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor mesotrione (RI = 3.5). In addition, 11 out of 19 E. indica biotypes exhibited multiple resistance to glyphosate. This research has identified the widespread occurrence of CyB resistance in E. indica, attributed to target-site mutations or enhanced metabolism. Moreover, certain biotypes have exhibited resistance to multiple herbicides or even cross-resistance. Consequently, there is an urgent need to implement diverse weed management practices to effectively combat the proliferation of this weed in rice fields.

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

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 are 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, although 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 100 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 analysed 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.

First Report of the Molecular Mechanism of Resistance to Tribenuron-Methyl in Silene conoidea L

Silene conoidea L. is an annual troublesome broadleaf weed in winter wheat fields in China. In recent years, field applications of tribenuron-methyl have been ineffective in controlling S. conoidea in Hebei Province, China. The aim of this study was to determine the molecular basis of tribenuron-methyl resistance in S. conoidea. Whole-plant response assays revealed that the resistant population (R) exhibited a higher level of resistance (382.3-fold) to tribenuron-methyl. The R population also showed high cross-resistance to other acetolactate synthase (ALS) inhibitors, including imazethapyr, bispyribac-sodium and florasulam. However, the R population could be controlled by the field-recommended rates of bentazone, MCPA, fluroxypyr, carfentrazone-ethyl and bromoxynil. In vitro ALS activity assays indicated that the tribenuron-methyl I₅₀ value for the R population was 18.5 times higher than those for the susceptible population (S). ALS gene sequencing revealed an amino acid mutation, Trp-574-Leu, in the R population. Pretreatment with the P450 inhibitor malathion indicated that the R population might have cytochrome P450-mediated metabolic resistance. These results suggest that the Trp-574-Leu mutation and P450-mediated enhanced metabolism coexist in S. conoidea to generate tribenuron-methyl resistance. This is the first time that target-site and non-target-site resistance to tribenuron-methyl has been reported in S. conoidea.

Diversity of Herbicide-Resistance Mechanisms of Avena fatua L. to Acetyl-CoA Carboxylase-Inhibiting Herbicides in the Bajio, Mexico

Herbicide resistance is an evolutionary process that affects entire agricultural regions’ yield and productivity. The high number of farms and the diversity of weed management can generate hot selection spots throughout the regions. Resistant biotypes can present a diversity of mechanisms of resistance and resistance factors depending on selective conditions inside the farm; this situation is similar to predictions by the geographic mosaic theory of coevolution. In Mexico, the agricultural region of the Bajio has been affected by herbicide resistance for 25 years. To date, Avena fatua L. is one of the most abundant and problematic weed species. The objective of this study was to determine the mechanism of resistance of biotypes with failures in weed control in 70 wheat and barley crop fields in the Bajio, Mexico. The results showed that 70% of farms have biotypes with target site resistance (TSR). The most common mutations were Trp–1999–Cys, Asp–2078–Gly, Ile–2041–Asn, and some of such mutations confer cross-resistance to ACCase-inhibiting herbicides. Metabolomic fingerprinting showed four different metabolic expression patterns. The results confirmed that in the Bajio, there exist multiple selection sites for both resistance mechanisms, which proves that this area can be considered as a geographic mosaic of resistance.

Multiple resistance to ACCase- and ALS-inhibiting herbicides in black-grass (Alopecurus myosuroides Huds.) in China

Two black-grass (Alopecurus myosuroides Huds.) populations (R2105 and R1027) that were suspected to be resistant to clodinafop-propargyl, an acetyl-CoAcarboxylase (ACCase) inhibitor, were found in winter wheat fields in China. Research was carried out to investigate whether resistance to clodinafop-propargyl was present and the molecular mechanism of herbicide resistance in these two populations. Dose-response assays confirmed high level resistance to clodinafop-propargyl in both R2105 and R1027 populations, with resistance indexes 25.1 and 22.1. ACCase gene sequence comparison revealed three amino acid mutations (Trp-1999-Leu, Ile-2041-Asn, or Asp-2078-Gly) in R2105 population and Ile-2041-Asn mutation in R1027 population. Sensitivity to other herbicides assays indicated that R2105 and R1027 populations were cross resistant to fenoxaprop-P-ethyl and multiple resistant to pyroxsulam and mesosulfuron-methyl. The ALS gene sequence analysis revealed that all resistant individuals in R2105 and R1027 populations had the Trp-574-Leu mutation. Applying malathion, significantly decreased the rate of metabolism of clodinafop-propargyl in both R2105 and R1027 populations. This is the first report of multiple resistance to ACCase- and ALS-inhibiting herbicides conferred by target-site mutations and enhanced metabolism in black-grass in China.

Genomic-based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America

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 (i) 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 (ii) 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 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 geographical associations with the Northern Plains and the other with 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.

Differences in Germination of ACCase-Resistant Biotypes Containing Isoleucine-1781-Leucine Mutation and Susceptible Biotypes of Wild Oat (Avena sterilis ssp. ludoviciana)

Herbicide resistance can affect seed germination and the optimal conditions required for seed germination, which in turn may impose a fitness cost in resistant populations. Winter wild oat [Avena sterilis L. ssp. ludoviciana (Durieu) Gillet and Magne] is a serious weed in cereal fields. In this study, the molecular basis of resistance to an ACCase herbicide, clodinafop-propargyl, in four A. ludoviciana biotypes was assessed. Germination differences between susceptible (S) and ACCase-resistant biotypes (WR₁, WR₂, WR₃, WR₄) and the effect of Isoleucine-1781-Leucine mutation on germination were also investigated through germination models. The results indicated that WR₁ and WR₄ were very highly resistant (RI > 214.22) to clodinafop-propargyl-contained Isoleucine to Leucine amino acid substitution. However, Isoleucine-1781-Leucine mutation was not detected in other very highly resistant biotypes. Germination studies indicated that resistant biotypes (in particular WR₁ and WR₄) had higher base water potentials than the susceptible one. This shows that resistant biotypes need more soil water to initiate their germination. However, the hydrotime constant for germination was higher in resistant biotypes than in the susceptible one in most cases, showing faster germination in susceptible biotypes. ACCase-resistant biotypes containing the Isoleucine-1781-Leucine mutation had lower seed weight but used more seed reserve to produce seedlings. Hence, integrated management practices such as stale seedbed and implementing it at the right time could be used to take advantage of the differential soil water requirement and relatively late germination characteristics of ACCase-resistant biotypes.

Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides

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 (F_ST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (F_IS = 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.

Agricultural adaptation in the native North American weed waterhemp, Amaranthus tuberculatus (Amaranthaceae)

There is increasing interest in documenting adaptation of weedy plant species to agricultural ecosystems, beyond the evolution of herbicide resistance. Waterhemp (Amaranthus tuberculatus) is a native plant of the Midwestern U.S. that began infesting agricultural fields in the 20th century within the central portion of its range. We hypothesized that the vegetative growth and reproductive traits of waterhemp from this heavily infested central region provide differential fitness benefits in agricultural environments. We collected seeds from across the species' native range, representing regions with varying degrees of waterhemp infestation, and planted them together in common garden soybean plots. A 2010 common garden experiment was conducted within the range of agriculturally weedy waterhemp (in Missouri), and a 2011 common garden experiment was conducted outside of this range (in Ohio). Days to flowering and flowering plant height, mature plant size data (height, number of branches, and length of the longest branch), and above-ground biomass were measured to estimate relative fitness. In both common garden locations, plants from regions where waterhemp occurs as an agricultural weed - including those from the heavily infested Mississippi Valley region (Iowa, Illinois, and Missouri) and the less severely infested Plains region (Nebraska, Kansas, and Oklahoma) - had higher relative performance in almost all fitness-related measures than plants from the Northeast region (Ohio, Michigan, and Ontario), which had little to no agriculturally weedy waterhemp at the time of our study. Further analysis revealed that fewer days to flowering in the Northeast populations can be largely accounted for by latitude of origin, suggesting a strong genetic influence on this reproductive trait. These findings suggest intraspecific variation in agricultural adaptation in a native U.S. weed, and support the use of agricultural weeds to study adaptation.

Evolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management

Intense selection by pesticides and antibiotics has resulted in a global epidemic of evolved resistance. In agriculture and medicine, using mixtures of compounds from different classes is widely accepted as optimal resistance management. However, this strategy may promote the evolution of more generalist resistance mechanisms. Here we test this hypothesis at a national scale in an economically important agricultural weed: blackgrass (Alopecurus myosuroides), for which herbicide resistance is a major economic issue. Our results reveal that greater use of herbicide mixtures is associated with lower levels of specialist resistance mechanisms, but higher levels of a generalist mechanism implicated in enhanced metabolism of herbicides with diverse modes of action. Our results indicate a potential evolutionary trade-off in resistance management, whereby attempts to reduce selection for specialist resistance traits may promote the evolution of generalist resistance. We contend that where specialist and generalist resistance mechanisms co-occur, similar trade-offs will be evident, calling into question the ubiquity of resistance management based on mixtures and combination therapies.

Mixtures of antibiotics or pesticides can help reduce the evolution of resistance to individual compounds. Here, Comont et al. show that in blackgrass, an important agricultural weed, herbicide mixtures do reduce specialized resistance but instead can select for a generalized resistance mechanism.

Trp2027Cys mutation evolves in Digitaria insularis with cross-resistance to ACCase inhibitors

Sourgrass (Digitaria insularis) is one of the most problematic weeds in South America because glyphosate resistance is widespread across most crop production regions. Acetyl coenzyme A carboxylase (ACCase)-inhibiting herbicides have been intensively used to manage D. insularis, which substantially increased selection pressure for this class of herbicides. We confirmed resistance to ACCase herbicides in a D. insularis population from Brazil and characterized its molecular basis. Resistant plants showed high level of resistance to haloxyfop (resistance factor, RF = 613-fold), low level of resistance to pinoxaden (RF = 3.6-fold), and no resistance to clethodim. A target-site mutation, Trp2027Cys, was found in the ACCase sequence from resistant plants. A protein homology model shows that the Trp2027Cys mutation is near the herbicide-binding pocket formed between two ACCase chains, and is predicted to obstruct the access of aryloxyphenoxypropionates (FOP) herbicides to the binding site. A qPCR-based single nucleotide polymorphism genotyping method was validated to discriminate susceptible (wild-type Trp2027) and resistant (mutant Cys2027) alleles. All resistant plants were homozygous for the mutation and the assay could be used for early detection of resistance in D. insularis field samples with suspected resistance to ACCase inhibitors.

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed

The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.

Growth behavior and glyphosate resistance level in 10 populations of Echinochloa colona in Australia

Recently, poor control of Echinochloa colona with glyphosate has been reported in no-till agriculture systems of the northern grain region (NGR) of Australia. Two experiments were conducted using 10 populations of E. colona selected from the NGR of Australia to understand differences in their growth behavior and resistance pattern. Growth studies revealed that these populations differed in plant height (53-70 cm plant-1), tiller production (30-52 tillers plant-1), leaf production (124-186 leaves plant-1) and seed head production (37-65 seed heads plant-1). Days taken to seed heads and shoot biomass in these populations ranged between 40-48 d and 21-27 g plant-1, respectively. Seed production in these populations ranged between 5380 and 10244 seeds plant-1; lowest for population B17/25 and highest for population B17/13. Correlation studies revealed that seed number plant-1 had a positive correlation with tiller number plant-1 (r = 0.73) and negative relation with days taken to seed head initiation (r = - 0.65). The glyphosate dose-response study showed a wide range of responses in these populations and the glyphosate dose required to kill 50% plants (LD50 values) was estimated between 161 to 2339 g a.e. glyphosate ha-1. LD50 values of populations B17/16, B 17/34 and B17/35 were 1086, 2339 and 1153 g ha-1, respectively, making them 6.7, 15.1 and 7.2-fold resistant to glyphosate compared with the susceptible population B17/37. Growth behavior and seed production potential in these populations had no correlation with the resistance index. These results suggest that some populations of E. colona are highly problematic; for example, population B17/34 was not only highly glyphosate-resistant, but also produced a high seed number (9300 seeds plant-1). This study demonstrated that there is a possibility of great risk with the increased use of glyphosate for managing E. colona in the NGR of Australia. The results warrant integrated weed management strategies and improved stewardship guidelines are required for managing glyphosate-resistant populations of E. colona and to restrict further movement of resistant populations to other regions of Australia.

The costs of human-induced evolution in an agricultural system

Pesticides have underpinned significant improvements in global food security, albeit with associated environmental costs. Currently, the yield benefits of pesticides are threatened as overuse has led to wide-scale evolution of resistance. Yet despite this threat, there are no large-scale estimates of crop yield losses or economic costs due to resistance. Here, we combine national-scale density and resistance data for the weed Alopecurus myosuroides (black-grass) with crop yield maps and a new economic model to estimate that the annual cost of resistance in England is £0.4bn in lost gross profit (2014 prices), and annual wheat yield loss due to resistance is 0.8 million tonnes. A total loss of herbicide control against black-grass would cost £1bn and 3.4 million tonnes of lost wheat yield annually. Worldwide, there are 253 herbicide-resistant weeds, so the global impact of resistance could be enormous. Our research provides an urgent case for national-scale planning to combat further evolution of resistance, and an incentive for policies focused on increasing yields through more sustainable food-production systems rather than relying so heavily on herbicides.

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

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.

Target-site and non-target-site-based resistance to tribenuron-methyl in multiply-resistant Myosoton aquaticum L

Myosoton aquaticum L., a widespread and competitive winter weed of wheat in China, has evolved resistance to many classes of herbicides. In one M. aquaticum population (AH03), collected from Anhui Province, where tribenuron-methyl and florasulam had been used to control this weed resistance to both herbicides had evolved. Compared with the sensitive population, HN03(S), the resistant (R) population, AH03, was highly resistant to tribenuron-methyl, flucarbazone-Na and pyroxsulam, moderately resistant to pyrithiobac‑sodium, and florasulam, and had low resistance to diflufenican. AH03 was still controlled by imazethapyr, 2,4-D butylate, fluroxypyr-meptyl, and isoproturon. Pretreatment with the P450 inhibitor malathion reduced the GR₅₀ value of tribenuron-methyl by 43% in the R population, and by 25% in the S population. This indicates that P450-mediated enhanced metabolism is one likely mechanism for tribenuron-methyl resistance in M. aquaticum. Glutathione-S-transferase (GST) activity could be induced by tribenuron-methyl in both the R and S populations. However, both the basal and induced GST activity of the R population was lower than that of the S population. The in vitro ALS assay confirmed that the ALS from the R plants showed a high resistance (52.93-fold) to tribenuron-methyl. ALS gene sequencing revealed a Pro197Ala substitution in the R plants. Based on the ALS gene sequence analysis, molecular markers were also developed to identify the specific Pro197Ala mutation. This population of M. aquaticum has multiple resistance and target-site (ALS Pro197Ala) and non-target-site resistance mechanisms contribute to tribenuron-methyl resistance.

Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

BACKGROUND

Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides.

RESULTS

We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants.

CONCLUSION

The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.

The power and potential of genomics in weed biology and management

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. © 2018 Society of Chemical Industry.

What good is weed diversity?

Should the declining diversity of weed communities in conventionally managed arable fields be regarded as a problem? The answer to this question has tended to divide researchers into those whose primary focus is on conserving farmland biodiversity and those whose goals are dictated by weed control and maximising yield. Here, we argue that, regardless of how weeds are perceived, there are common ecological principles that should underpin any approach to managing weed communities, and, based on these principles, increasing in-field weed diversity could be advantageous agronomically as well as environmentally. We hypothesise that a more diverse weed community will be less competitive, less prone to dominance by highly adapted, herbicide-resistant species and that the diversity of the weed seedbank will be indicative of the overall sustainability of the cropping system. Common to these hypotheses is the idea that the intensification of agriculture has been accompanied by a homogenisation of cropping systems and landscapes, accounting for both declines in weed diversity and the reduced resilience of cropping systems (including the build-up of herbicide resistance). As such, weed communities represent a useful indicator of the success of rediversifying systems at multiple scales, which will be a central component of making agriculture and weed control more sustainable.

Reviewing research priorities in weed ecology, evolution and management: a horizon scan

Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre-submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio-economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system-oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs.

A mosaic of phenotypic variation in giant ragweed (Ambrosia trifida): Local- and continental-scale patterns in a range-expanding agricultural weed

Spatial patterns of trait variation across a species' range have implications for population success and evolutionary change potential, particularly in range-expanding and weedy species that encounter distinct selective pressures at large and small spatial scales simultaneously. We investigated intraspecific trait variation in a common garden experiment with giant ragweed (Ambrosia trifida), a highly variable agricultural weed with an expanding geographic range and broad ecological amplitude. Our study included paired populations from agricultural and natural riparian habitats in each of seven regions ranging east to west from the core of the species' distribution in central Ohio to southeastern Minnesota, which is nearer the current invasion front. We observed trait variation across both large- and small-scale putative selective gradients. At large scales, giant ragweed populations from the westernmost locations were nearly four times more fecund and had a nearly 50% increase in reproductive allocation compared to populations from the core. The degree of surface texture on fruits also declined from east to west. Greater fecundity in the west represents a putative trade-off between fruit size and fruit number across the study region, although no such trade-off was found across individual plants. This pattern may effectively result in greater propagule pressure closer to the invasion front. At smaller spatial scales, plants from agricultural populations emerged later and were smaller than plants from riparian populations. However, because plants from agricultural populations allocated more biomass to reproduction, total fecundity did not differ across habitats. Our emergence data are consistent with previous observations showing delayed emergence in agricultural compared to natural populations; thus evolutionary change may be predictable as giant ragweed continues spreading into agricultural fields throughout North America. These shifts in life-history strategy apparently bear no fecundity cost, suggesting that giant ragweed's success can be attributed at least in part to its substantial adaptive potential.

Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)

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.

Simulating changes in cropping practises in conventional and glyphosate-tolerant maize. I. Effects on weeds

Herbicide-tolerant (HT) crops such as those tolerant to glyphosate simplify weed management and make it more efficient, at least at short-term. Overreliance on the same herbicide though leads to the spread of resistant weeds. Here, the objective was to evaluate, with simulations, the impact on the advent of glyphosate resistance in weeds of modifications in agricultural practises resulting from introducing HT maize into cropping systems. First, we included a single-gene herbicide resistance submodel in the existing multispecific FLORSYS model. Then, we (1) simulated current conventional and probable HT cropping systems in two European regions, Aquitaine and Catalonia, (2) compared these systems in terms of glyphosate resistance, (3) identified pertinent cultural practises influencing glyphosate resistance, and (4) investigated correlations between cultural practises and species traits, using RLQ analyses. The simulation study showed that, during the analysed 28 years, (1) glyphosate spraying only results in glyphosate resistance in weeds when combined with other cultural factors favouring weed infestation, particularly no till; (2) pre-sowing glyphosate applications select more for herbicide resistance than post-sowing applications on HT crops; and (3) glyphosate spraying selects more for species traits avoiding exposure to the herbicide (e.g. delayed early growth, small leaf area) or compensating for fitness costs (e.g. high harvest index) than for actual resistance to glyphosate, (4) actual resistance is most frequent in species that do not avoid glyphosate, either via plant size or timing, and/or in less competitive species, (5) in case of efficient weed control measures, actual resistance proliferates best in outcrossing species. An advice table was built, with the quantitative, synthetic ranking of the crop management effects in terms of glyphosate-resistance management, identifying the optimal choices for each management technique.

Migration by seed dispersal of ACCase-inhibitor-resistant Avena fatua in north-western Mexico

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 hypothesised 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 through 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 × 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 A. fatua in the Valle de Hermosillo, SON, are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds. © 2016 Society of Chemical Industry.

Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis

Non-target-site resistance (NTSR) to herbicides is a worldwide concern for weed control. However, as the dominant NTSR mechanism in weeds, metabolic resistance is not yet well-characterized at the genetic level. For this study, we have identified a shortawn foxtail (Alopecurus aequalis Sobol.) population displaying both TSR and NTSR to mesosulfuron-methyl and fenoxaprop-P-ethyl, yet the molecular basis for this NTSR remains unclear. To investigate the mechanisms of metabolic resistance, an RNA-Seq transcriptome analysis was used to find candidate genes that may confer metabolic resistance to the herbicide mesosulfuron-methyl in this plant population. The RNA-Seq libraries generated 831,846,736 clean reads. The de novo transcriptome assembly yielded 95,479 unigenes (averaging 944 bp in length) that were assigned putative annotations. Among these, a total of 29,889 unigenes were assigned to 67 GO terms that contained three main categories, and 14,246 unigenes assigned to 32 predicted KEGG metabolic pathways. Global gene expression was measured using the reads generated from the untreated control (CK), water-only control (WCK), and mesosulfuron-methyl treatment (T) of R and susceptible (S). Contigs that showed expression differences between mesosulfuron-methyl-treated R and S biotypes, and between mesosulfuron-methyl-treated, water-treated and untreated R plants were selected for further quantitative real-time PCR (qRT-PCR) validation analyses. Seventeen contigs were consistently highly expressed in the resistant A. aequalis plants, including four cytochrome P450 monooxygenase (CytP450) genes, two glutathione S-transferase (GST) genes, two glucosyltransferase (GT) genes, two ATP-binding cassette (ABC) transporter genes, and seven additional contigs with functional annotations related to oxidation, hydrolysis, and plant stress physiology. These 17 contigs could serve as major candidate genes for contributing to metabolic mesosulfuron-methyl resistance; hence they deserve further functional study. This is the first large-scale transcriptome-sequencing study to identify NTSR genes in A. aequalis that uses the Illumina platform. This work demonstrates that NTSR is likely driven by the differences in the expression patterns of a set of genes. The assembled transcriptome data presented here provide a valuable resource for A. aequalis biology, and should facilitate the study of herbicide resistance at the molecular level in this and other weed species.

Choosing the best cropping systems to target pleiotropic effects when managing single-gene herbicide resistance in grass weeds. A blackgrass simulation study

BACKGROUND

Managing herbicide-resistant weeds is becoming increasingly difficult. Here we adapted the weed dynamics model AlomySys to account for experimentally measured fitness costs linked to mutants of target-site resistance to acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides in Alopecurus myosuroides. We ran simulations to test how effectively cultural practices manage resistance.

RESULTS

Simulations of an oilseed rape/winter wheat/winter barley rotation showed that, when replacing one of the seven applied herbicides with an ACCase-inhibiting one, resistant mutants exceeded 1 plant m(-2) , with a probability of 40%, after an average of 18 years. This threshold was always exceeded when three or four ACCase-inhibiting herbicides were used, after an average of 8 and 6 years respectively. With reduced herbicide rates or suboptimal spraying conditions, resistance occurred 1-3 years earlier in 50% of simulations. Adding spring pea to the rotation or yearly mouldboard ploughing delayed resistance indefinitely in 90 and 60% of simulations respectively. Ploughing also modified the genetic composition of the resistant population by selecting a previously rare mutant that presented improved pre-emergent growth. The prevalence of the mutations was influenced more by their associated fitness cost or benefit than by the number of ACCase-inhibiting herbicides to which they conferred resistance.

CONCLUSION

Simulations allowed us to rank weed management practices and suggest that pleiotropic effects are extremely important for understanding the frequency of herbicide resistance in the population. © 2016 Society of Chemical Industry.

Trends and Challenges in Pesticide Resistance Detection

Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides while maintaining pesticide efficacy. This goal requires monitoring 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.

Cross-resistance to prosulfocarb + S-metolachlor and pyroxasulfone selected by either herbicide in Lolium rigidum

BACKGROUND

Weeds can be a greater constraint to crop production than animal pests and pathogens. Pre-emergence herbicides are crucial in many cropping systems to control weeds that have evolved resistance to selective post-emergence herbicides. In this study we assessed the potential to evolve resistance to the pre-emergence herbicides prosulfocarb + S-metolachlor or pyroxasulfone in 50 individual field Lolium rigidum populations collected in a random survey in Western Australia prior to commercialisation of these pre-emergence herbicides.

RESULTS

This study shows for the first time that in randomly collected L. rigidum field populations the selection with either prosulfocarb + S-metolachlor or pyroxasulfone can result in concomitant evolution of resistance to both prosulfocarb + S-metolachlor and pyroxasulfone after three generations.

CONCLUSIONS

In the major weed L. rigidum, traits conferring resistance to new herbicides can be present before herbicide commercialisation. Proactive and multidisciplinary research (evolutionary ecology, modelling and molecular biology) is required to detect and analyse resistant populations before they can appear in the field. Several studies show that evolved cross-resistance in weeds is complex and often unpredictable. Thus, long-term management of cross-resistant weeds must be achieved through heterogeneity of selection by effective chemical, cultural and physical weed control strategies that can delay herbicide resistance evolution. © 2016 Society of Chemical Industry.

Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

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.

ACCase mutations in Avena sterilis populations and their impact on plant fitness

Avena sterilis (sterile oat) populations originating from wheat-growing regions of Greece, developed resistance to fenoxaprop, clodinafop and other herbicides. The partial ACCase gene sequence revealed six point mutations (Ile-1781-Leu, Trp-1999-Cys, Trp-2027-Cys, Ile-2041-Asn, Asp-2078-Gly, and Cys-2088-Arg) in 24 out of the 26 resistant (R) populations, confirming the molecular mechanism of resistance to ACCase-inhibiting herbicides. However, DNA sequence of two R populations did not reveal any known ACCase mutations, suggesting possible presence of unknown mutation or metabolism-based mechanism of resistance. The Cys-2088-Arg mutation is the first record for ACCase mutant conferring target-site resistance in A. sterilis worldwide. The evaluation of 12 R and 6 susceptible (S) populations under non-competitive field conditions did not indicate consistent mean growth rate differences, whereas the pot evaluation of the same (12 R and 6 S) populations grown in competition with wheat or in pure stands showed significant growth (fresh weight and panicle number) differences between six S populations and between six R populations containing the same ACCase mutation (Ile-2041-Asn). Finally, one S and five R (Trp-1999-Cys, Trp-2027-Cys, Ile-2041-Asn, Asp-2078-Gly, and Cys-2088-Arg) populations grown under field competitive conditions indicated fresh weight and panicle number differences in competition with other populations as compared with pure stands. These findings suggest clearly that the inconsistent fitness differences between R and S A. sterilis populations are not related with the ACCase resistance trait but they may result from other non-resistance fitness traits selected in their different geographical locations.

The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: Evidence for resistance hotspots and low genetic differentiation across the landscape

Strong human-mediated selection via herbicide application in agroecosystems has repeatedly led to the evolution of resistance in weedy plants. Although resistance can occur among separate populations of a species across the landscape, the spatial scale of resistance in many weeds is often left unexamined. We assessed the potential that resistance to the herbicide glyphosate in the agricultural weed Ipomoea purpurea has evolved independently multiple times across its North American range. We examined both adaptive and neutral genetic variations in 44 populations of I. purpurea by pairing a replicated dose–response greenhouse experiment with SSR genotyping of experimental individuals. We uncovered a mosaic pattern of resistance across the landscape, with some populations exhibiting high-survival postherbicide and other populations showing high death. SSR genotyping revealed little evidence of isolation by distance and very little neutral genetic structure associated with geography. An approximate Bayesian computation (ABC) analysis uncovered evidence for migration and admixture among populations before the widespread use of glyphosate rather than the very recent contemporary gene flow. The pattern of adaptive and neutral genetic variations indicates that resistance in this mixed-mating weed species appears to have evolved in independent hotspots rather than through transmission of resistance alleles across the landscape.

ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass)

Background

Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available.

Results

RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein.

Conclusions

Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.

Using next-generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate-synthase (ALS)-based resistance in barnyard grass, a polyploid grass weed

BACKGROUND

Next-generation sequencing (NGS) technologies offer tremendous possibilities for accurate detection of mutations endowing pesticide resistance, yet their use for this purpose has not emerged in crop protection. This study aims at promoting NGS use for pesticide resistance diagnosis. It describes a simple procedure accessible to virtually any scientist and implementing freely accessible programs for the analysis of NGS data.

RESULTS

Three PCR amplicons encompassing seven codons of the acetolactate-synthase gene crucial for herbicide resistance were sequenced using non-quantified pools of crude DNA extracts from 40 plants in each of 28 field populations of barnyard grass, a polyploid weed. A total of 63,959 quality NGS sequence runs were obtained using the 454 technology. Three herbicide-resistance-endowing mutations (Pro-197-Ser, Pro-197-Leu and/or Trp-574-Leu) were identified in seven populations. The NGS results were confirmed by individual plant Sanger sequencing.

CONCLUSION

This work demonstrated the feasibility of NGS-based detection of pesticide resistance, and the advantages of NGS compared with other molecular biology techniques for analysing large numbers of individuals. NGS-based resistance diagnosis has the potential to play a substantial role in monitoring resistance, maintaining pesticide efficacy and optimising pesticide applications.

Expanding the eco-evolutionary context of herbicide resistance research

The potential for human-driven evolution in economically and environmentally important organisms in medicine, agriculture and conservation management is now widely recognised. The evolution of herbicide resistance in weeds is a classic example of rapid adaptation in the face of human-mediated selection. Management strategies that aim to slow or prevent the evolution of herbicide resistance must be informed by an understanding of the ecological and evolutionary factors that drive selection in weed populations. Here, we argue for a greater focus on the ultimate causes of selection for resistance in herbicide resistance studies. The emerging fields of eco-evolutionary dynamics and applied evolutionary biology offer a means to achieve this goal and to consider herbicide resistance in a broader and sometimes novel context. Four relevant research questions are presented, which examine (i) the impact of herbicide dose on selection for resistance, (ii) plant fitness in herbicide resistance studies, (iii) the efficacy of herbicide rotations and mixtures and (iv) the impacts of gene flow on resistance evolution and spread. In all cases, fundamental ecology and evolution have the potential to offer new insights into herbicide resistance evolution and management.

Resistance to acetyl-CoA carboxylase-inhibiting herbicides

Resistance to acetyl-CoA carboxylase herbicides is documented in at least 43 grass weeds and is particularly problematic in Lolium, Alopecurus and Avena species. Genetic studies have shown that resistance generally evolves independently and can be conferred by target-site mutations at ACCase codon positions 1781, 1999, 2027, 2041, 2078, 2088 and 2096. The level of resistance depends on the herbicides, recommended field rates, weed species, plant growth stages, specific amino acid changes and the number of gene copies and mutant ACCase alleles. Non-target-site resistance, or in essence metabolic resistance, is prevalent, multigenic and favoured under low-dose selection. Metabolic resistance can be specific but also broad, affecting other modes of action. Some target-site and metabolic-resistant biotypes are characterised by a fitness penalty. However, the significance for resistance regression in the absence of ACCase herbicides is yet to be determined over a practical timeframe. More recently, a fitness benefit has been reported in some populations containing the I1781L mutation in terms of vegetative and reproductive outputs and delayed germination. Several DNA-based methods have been developed to detect known ACCase resistance mutations, unlike metabolic resistance, as the genes remain elusive to date. Therefore, confirmation of resistance is still carried out via whole-plant herbicide bioassays. A growing number of monocotyledonous crops have been engineered to resist ACCase herbicides, thus increasing the options for grass weed control. While the science of ACCase herbicide resistance has progressed significantly over the past 10 years, several avenues provided in the present review remain to be explored for a better understanding of resistance to this important mode of action.

DNA analysis of herbarium Specimens of the grass weed Alopecurus myosuroides reveals herbicide resistance pre-dated herbicides

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications.

Role of a novel I1781T mutation and other mechanisms in conferring resistance to acetyl-CoA carboxylase inhibiting herbicides in a black-grass population

Background

Knowledge of the mechanisms of herbicide resistance is important for designing long term sustainable weed management strategies. Here, we have used an integrated biology and molecular approach to investigate the mechanisms of resistance to acetyl-CoA carboxylase inhibiting herbicides in a UK black-grass population (BG2).

Methodology/Principal Findings

Comparison between BG2 phenotypes using single discriminant rates of herbicides and genotypes based on ACCase gene sequencing showed that the I1781L, a novel I1781T, but not the W2027C mutations, were associated with resistance to cycloxydim. All plants were killed with clethodim and a few individuals containing the I1781L mutation were partially resistant to tepraloxydim. Whole plant dose response assays demonstrated that a single copy of the mutant T1781 allele conferred fourfold resistance levels to cycloxydim and clodinafop-propargyl. In contrast, the impact of the I1781T mutation was low (Rf = 1.6) and non-significant on pinoxaden. BG2 was also characterised by high levels of resistance, very likely non-target site based, to the two cereal selective herbicides clodinafop-propargyl and pinoxaden and not to the poorly metabolisable cyclohexanedione herbicides. Analysis of 480 plants from 40 cycloxydim resistant black grass populations from the UK using two very effective and high throughput dCAPS assays established for detecting any amino acid changes at the 1781 ACCase codon and for positively identifying the threonine residue, showed that the occurrence of the T1781 is extremely rare compared to the L1781 allele.

Conclusion/Significance

This study revealed a novel mutation at ACCase codon position 1781 and adequately assessed target site and non-target site mechanisms in conferring resistance to several ACCase herbicides in a black-grass population. It highlights that over time the level of suspected non-target site resistance to some cereal selective ACCase herbicides have in some instances surpassed that of target site resistance, including the one endowed by the most commonly encountered I1781L mutation.

The presence of two different target-site resistance mechanisms in individual plants of Alopecurus myosuroides Huds., identified using a quick molecular test for the characterisation of six ALS and seven ACCase SNPs

BACKGROUND

Target-site resistance to ALS- and ACCase-inhibiting herbicides in the grass weed Alopecurus myosuroides is associated with well-characterised allelic variants encoding ALS- and ACCase-based resistance. The potential for combined ALS and ACCase resistance presents a threat to future control, given the extent to which these herbicides are used. The authors present a primer extension method for rapid detection of known resistance-conferring substitutions.

RESULTS

Individuals showing combined resistance to field-rate mesosulfuron + iodosulfuron and cycloxydim were identified in four field-collected populations, with proportions ranging from 30 to 100%. Genotyping with the SNaPshot primer extension kit showed the T197 and L574 ALS and L1781 ACCase isoforms to be associated with ALS and ACCase resistance whenever they occurred.

CONCLUSION

Combined ALS and ACCase target-site resistance threatens future control of A. myosuroides. The SNaPshot extension assay provides a reliable new multiplexable method for characterising known allelic variants of the ALS and ACCase genes of A. myosuroides. The method offers significant advantages over both CAPS/dCAPS and PASA in that full genotyping can be accomplished at any nucleotide position using a single extension primer.

A new insight into arable weed adaptive evolution: mutations endowing herbicide resistance also affect germination dynamics and seedling emergence

BACKGROUND AND AIMS

Selective pressures exerted by agriculture on populations of arable weeds foster the evolution of adaptive traits. Germination and emergence dynamics and herbicide resistance are key adaptive traits. Herbicide resistance alleles can have pleiotropic effects on a weed's life cycle. This study investigated the pleiotropic effects of three acetyl-coenzyme A carboxylase (ACCase) alleles endowing herbicide resistance on the seed-to-plant part of the life cycle of the grass weed Alopecurus myosuroides.

METHODS

In each of two series of experiments, A. myosuroides populations with homogenized genetic backgrounds and segregating for Leu1781, Asn2041 or Gly2078 ACCase mutations which arose independently were used to compare germination dynamics, survival in the soil and seedling pre-emergence growth among seeds containing wild-type, heterozygous and homozygous mutant ACCase embryos.

KEY RESULTS

Asn2041 ACCase caused no significant effects. Gly2078 ACCase major effects were a co-dominant acceleration in seed germination (1·25- and 1·10-fold decrease in the time to reach 50 % germination (T50) for homozygous and heterozygous mutant embryos, respectively). Segregation distortion against homozygous mutant embryos or a co-dominant increase in fatal germination was observed in one series of experiments. Leu1781 ACCase major effects were a co-dominant delay in seed germination (1·41- and 1·22-fold increase in T50 for homozygous and heterozygous mutant embryos, respectively) associated with a substantial co-dominant decrease in fatal germination.

CONCLUSIONS

Under current agricultural systems, plants carrying Leu1781 or Gly2078 ACCase have a fitness advantage conferred by herbicide resistance that is enhanced or counterbalanced, respectively, by direct pleiotropic effects on the plant phenology. Pleiotropic effects associated with mutations endowing herbicide resistance undoubtedly play a significant role in the evolutionary dynamics of herbicide resistance in weed populations. Mutant ACCase alleles should also prove useful to investigate the role played by seed storage lipids in the control of seed dormancy and germination.

Evolution and spread of glyphosate resistance in Conyza canadensis in California

Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA), and the genetic diversity and population structure and history using microsatellite markers. Frequencies of resistant individuals in 42 sampled populations were positively correlated with the size of GWPA within counties. Analyses of population genetic structure also supported spread of resistance in these areas. Bayesian clustering and approximate Bayesian computation (ABC) analyses revealed multiple independent origins of resistance within the Central Valley. Based on parameter estimation in the ABC analyses, resistant genotypes underwent expansion after glyphosate use began in agriculture, but many years before it was detected. Thus, diversity in weed control practices prior to herbicide regulation in GWPA probably kept resistance frequencies low. Regionally coordinated efforts to reduce seed dispersal and selection pressure are needed to manage glyphosate resistance in C. canadensis.

A novel W1999S mutation and non-target site resistance impact on acetyl-CoA carboxylase inhibiting herbicides to varying degrees in a UK Lolium multiflorum population

BACKGROUND

Acetyl-CoA carboxylase (ACCase) inhibiting herbicides are important products for the post-emergence control of grass weed species in small grain cereal crops. However, the appearance of resistance to ACCase herbicides over time has resulted in limited options for effective weed control of key species such as Lolium spp. In this study, we have used an integrated biological and molecular biology approach to investigate the mechanism of resistance to ACCase herbicides in a Lolium multiflorum Lam. from the UK (UK21).

METHODOLOGY/PRINCIPAL FINDINGS

The study revealed a novel tryptophan to serine mutation at ACCase codon position 1999 impacting on ACCase inhibiting herbicides to varying degrees. The W1999S mutation confers dominant resistance to pinoxaden and partially recessive resistance to cycloxydim and sethoxydim. On the other hand, plants containing the W1999S mutation were sensitive to clethodim and tepraloxydim. Additionally population UK21 is characterised by other resistance mechanisms, very likely non non-target site based, affecting several aryloxyphenoxyproprionate (FOP) herbicides but not the practical field rate of pinoxaden. The positive identification of wild type tryptophan and mutant serine alleles at ACCase position 1999 could be readily achieved with an original DNA based derived cleaved amplified polymorphic sequence (dCAPS) assay that uses the same PCR product but two different enzymes for positively identifying the wild type tryptophan and mutant serine alleles identified here.

CONCLUSION/SIGNIFICANCE

This paper highlights intrinsic differences between ACCase inhibiting herbicides that could be exploited for controlling ryegrass populations such as UK21 characterised by compound-specific target site and non-target site resistance.

Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade

Non-target-site-based resistance (NTSR) can confer unpredictable cross-resistance to herbicides. However, the genetic determinants of NTSR remain poorly known. The current, urgent challenge for weed scientists is thus to elucidate the bases of NTSR so that detection tools are developed, the evolution of NTSR is understood, the efficacy of the shrinking herbicide portfolio is maintained and integrated weed management strategies, including fully effective herbicide applications, are designed and implemented. In this paper, the importance of NTSR in resistance to herbicides is underlined. The most likely way in which NTSR evolves-by accumulation of different mechanisms within individual plants-is described. The NTSR mechanisms, which can interfere with herbicide penetration, translocation and accumulation at the target site, and/or protect the plant against the consequences of herbicide action, are then reviewed. NTSR is a part of the plant stress response. As such, NTSR is a dynamic process unrolling over time that involves 'protectors' directly interfering with herbicide action, and also regulators controlling 'protector' expression. NTSR is thus a quantitative trait. On this basis, a three-step procedure is proposed, based on the use of the 'omics' (genomics, transcriptomics, proteomics or metabolomics), to unravel the genetic bases of NTSR.

Validation of a set of reference genes to study response to herbicide stress in grasses

Background

Non-target-site based resistance to herbicides is a major threat to the chemical control of agronomically noxious weeds. This adaptive trait is endowed by differences in the expression of a number of genes in plants that are resistant or sensitive to herbicides. Quantification of the expression of such genes requires normalising qPCR data using reference genes with stable expression in the system studied as internal standards. The aim of this study was to validate reference genes in Alopecurus myosuroides, a grass (Poaceae) weed of economic and agronomic importance with no genomic resources.

Results

The stability of 11 candidate reference genes was assessed in plants resistant or sensitive to herbicides subjected or not to herbicide stress using the complementary statistical methods implemented by NormFinder, BestKeeper and geNorm. Ubiquitin, beta-tubulin and glyceraldehyde-3-phosphate dehydrogenase were identified as the best reference genes. The reference gene set accuracy was confirmed by analysing the expression of the gene encoding acetyl-coenzyme A carboxylase, a major herbicide target enzyme, and of an herbicide-induced gene encoding a glutathione-S-transferase.

Conclusions

This is the first study describing a set of reference genes (ubiquitin, beta-tubulin and glyceraldehyde-3-phosphate dehydrogenase) with a stable expression under herbicide stress in grasses. These genes are also candidate reference genes of choice for studies seeking to identify stress-responsive genes in grasses.

Parallel Ecological Speciation in Plants?

Populations that have independently evolved reproductive isolation from their ancestors while remaining reproductively cohesive have undergone parallel speciation. A specific type of parallel speciation, known as parallel ecological speciation, is one of several forms of evidence for ecology's role in speciation. In this paper we search the literature for candidate examples of parallel ecological speciation in plants. We use four explicit criteria (independence, isolation, compatibility, and selection) to judge the strength of evidence for each potential case. We find that evidence for parallel ecological speciation in plants is unexpectedly scarce, especially relative to the many well-characterized systems in animals. This does not imply that ecological speciation is uncommon in plants. It only implies that evidence from parallel ecological speciation is rare. Potential explanations for the lack of convincing examples include a lack of rigorous testing and the possibility that plants are less prone to parallel ecological speciation than animals.