Dominance variation across six herbicides of the Arabidopsis thaliana csr1-1 and csr1-2 resistance alleles

Dominance of a resistance trait can be defined as a measure of the relative position of the phenotype of the heterozygote RS compared with the phenotype of the two corresponding homozygotes, SS and RR. This parameter has been shown to have primary importance in the dynamics of pesticide resistance evolution. Literature on insecticide resistance suggests that dominance levels in the presence of insecticide vary greatly from completely recessive to completely dominant. With insecticides, both the chemical applied and the dosages used have been demonstrated to affect the dominance. By contrast, almost all herbicide resistances have been found to be inherited as partially to totally dominant traits. This discrepancy between weeds and insects may partly result from the methodologies applied to measure the dominance, ie a single dose for herbicide versus several doses for insecticide. Using two well-known resistances (csr1-1 and csr1-2) to acetolactate synthase (ALS) inhibitors in Arabidopsis thaliana (L) Heynh (mouse-ear cress), we used several herbicide doses to determine the dominance level to six ALS-inhibiting herbicides. The dominance level in the presence of herbicide varied from completely dominant to completely recessive, depending on the resistance allele and the herbicide tested. The dominance of the csr1-1 and csr1-2 resistance alleles ranged from 0 (completely recessive) to 1.1 (dominant) and from 0 to 0.3 (partially dominant), respectively. The recessivity of some resistance alleles in the presence of herbicide could lead to the development of improved resistance management in order to delay or avoid herbicide resistance evolution, especially in the control of outcrossing weed species.     

Simulating evolution of glyphosate resistance in Lolium rigidum I: population biology of a rare resistance trait

Despite frequent use for the past 25 years, resistance to glyphosate has evolved in few weed biotypes. The propensity for evolution of resistance is not the same for all herbicides, and glyphosate has a relatively low resistance risk. The reasons for these differences are not entirely understood. A previously published two‐herbicide resistance model has been modified to explore biological and management factors that account for observed rates of evolution of glyphosate resistance. Resistance to a post‐emergence herbicide was predicted to evolve more rapidly than it did to glyphosate, even when both were applied every year and had the same control efficacy. Glyphosate is applied earlier in the growing season when fewer weeds have emerged and hence exerts less selection pressure on populations. The evolution of glyphosate resistance was predicted to arise more rapidly when glyphosate applications were later in the growing season. In simulations that assumed resistance to the post‐emergence herbicide did not evolve, the evolution of glyphosate resistance was less rapid, because post‐emergence herbicides were effectively controlling rare glyphosate‐resistant individuals. On their own, these management‐related factors could not entirely account for rates of evolution of resistance to glyphosate observed in the field. In subsequent analyses, population genetic parameter values (initial allele frequency, dominance and fitness) were selected on the basis of empirical data from a glyphosate‐resistant Lolium rigidum population. Predicted rates of evolution of resistance were similar to those observed in the field. Together, the timing of glyphosate applications, the rarity of glyphosate‐resistant mutants, the incomplete dominance of glyphosate‐resistant alleles and pleiotropic fitness costs associated with glyphosate resistance, all contribute to its relatively slow evolution in the field.     

杂草对AHAS抑制剂的抗药性分子机理研究进展

除草剂在田间的重复及不合理使用,导致了杂草抗药性的发生和发展。其中AHAS抑制剂由于靶标单一,抗性发展十分迅速。截至2009年,已有103种杂草对AHAS抑制剂产生了抗药性,占19类化学除草剂总抗药性杂草生物型的近1/3。从AHAS基因突变位点及种类与杂草抗药性水平的关系、AHAS基因突变与AHAS酶活性的关系、AHAS基因拷贝数与杂草抗药性的关系以及AHAS酶与除草剂结合前后的三维结构等方面,综述了杂草对AHAS抑制剂产生抗药性的机理,旨在为AHAS抑制剂抗性研究提供参考。并对自然种群目标基因的等位基因检测技术(ECOTILLING)和衍生型酶切扩增多态性序列(dCAPS)两种通过检测等位基因多态性的手段快速诊断抗药性杂草的新技术进行了介绍,讨论了延缓杂草抗药性发生和发展的策略。     

Simulation modelling to understand the evolution and management of glyphosate resistance in weeds

BACKGROUND: A simulation model is used to explore the influence of biological, ecological, genetic and operational (management) factors on the probability and rate of glyphosate resistance in model weed species. RESULTS: Glyphosate use for weed control prior to crop emergence is associated with low risks of resistance. These low risks can be further reduced by applying glyphosate in sequence with other broad-spectrum herbicides prior to crop seeding. Post-emergence glyphosate use, associated with glyphosate-resistant crops, very significantly increases risks of resistance evolution. Annual rotation with conventional crops reduces these risks, but the proportion of resistant populations can only be reduced to close to zero by mixing two of three post-emergence glyphosate applications with alternative herbicide modes of action. Weed species that are prolific seed producers with high seed bank turnover rates are most at risk of glyphosate resistance evolution. The model is especially sensitive to the initial frequency of R alleles, and other genetic and reproductive parameters, including weed breeding system, dominance of the resistance trait and relative fitness, influence rates of resistance. CONCLUSION: Changing patterns of glyphosate use associated with glyphosate-resistant crops are increasing risks of evolved glyphosate resistance. Strategies to mitigate these risks can be explored with simulation models. Models can also be used to identify weed species that are most at risk of evolving glyphosate resistance.     

Combining a weed traits database with a population dynamics model predicts shifts in weed communities

A functional approach to predicting shifts in weed floras in response to management or environmental change requires the combination of data on weed traits with analytical frameworks that capture the filtering effect of selection pressures on traits. A weed traits database (WTDB) was designed, populated and analysed, initially using data for 19 common European weeds, to begin to consolidate trait data in a single repository. The initial choice of traits was driven by the requirements of empirical models of weed population dynamics to identify correlations between traits and model parameters. These relationships were used to build a generic model, operating at the level of functional traits, to simulate the impact of increasing herbicide and fertiliser use on virtual weeds along gradients of seed weight and maximum height. The model generated ‘fitness contours’ (defined as population growth rates) within this trait space in different scenarios, onto which two sets of weed species, defined as common or declining in the UK, were mapped. The effect of increasing inputs on the weed flora was successfully simulated; 77% of common species were predicted to have stable or increasing populations under high fertiliser and herbicide use, in contrast with only 29% of the species that have declined. Future development of the WTDB will aim to increase the number of species covered, incorporate a wider range of traits and analyse intraspecific variability under contrasting management and environments.     

Relationship between weed dormancy and herbicide rotations: implications in resistance evolution

It is suggested that selection for late germinating seed cohorts is significantly associated with herbicide resistance in some cropping systems. In turn, it is conceivable that rotating herbicide modes of action selects for populations with mutations for increased secondary dormancy, thus partially overcoming the delaying effect of rotation on resistance evolution. Modified seed dormancy could affect management strategies – like herbicide rotation – that are used to prevent or control herbicide resistance. Here, we review the literature for data on seed dormancy and germination dynamics of herbicide‐resistant versus susceptible plants. Few studies use plant material with similar genetic backgrounds, so there are few really comparative data. Increased dormancy and delayed germination may co‐occur with resistance to ACCase inhibitors, but there is no clear‐cut link with resistance to other herbicide classes. Population shifts are due in part to pleiotropic effects of the resistance genes, but interaction with the cropping system is also possible. We provide an example of a model simulation that accounts for genetic diversity in the dormancy trait, and subsequent consequences for various cropping systems. We strongly recommend adding more accurate and detailed mechanistic modelling to the current tools used today to predict the efficiency of prevention and management of herbicide resistance. These models should be validated through long‐term experimental designs including mono‐herbicide versus chemical rotation in the field. © 2017 Society of Chemical Industry     

Estimating the outcrossing rate of Cyperus difformis using resistance to ALS-inhibiting herbicides and molecular markers

Cyperus difformis (smallflower umbrella sedge) is an economically important weed of rice in California where its control has recently been complicated by the evolution of herbicide resistance. Knowledge of the mating system of this weed is needed to elucidate the dynamics of resistance evolution and to design mitigation strategies that delay its occurrence. The aim of this study was to estimate the outcrossing rate of C. difformis using molecular and phenotypic markers. Outcrossing rates were estimated in natural field populations using sequence-related amplified polymorphism (SRAP) molecular markers and in glasshouse and field experiments using resistance to the acetolactate synthase-inhibiting herbicide bensulfuron-methyl as a phenotypic marker. Using SRAP markers, the multilocus ( t _m) and average single-locus ( t _s) outcrossing rates varied from 0.014 to 0.025 and from 0.008 to 0.012, respectively, among natural weed populations in rice fields. Using resistance to bensulfuron-methyl as a genetic marker, the average C. difformis outcrossing rate estimated was 0.009 in the glasshouse and 0.0084 in the field. These results indicate that C. difformis is a highly self-fertilising species. Therefore, the primary mechanism by which genes for herbicide resistance can be transferred among C. difformis populations in different rice fields is probably seed dispersal. Weed management should emphasise prevention of seed production and dispersal to preclude the further spread and evolution of resistance in C. difformis .     

Effect of exposure period on degree of dominance of phosphine resistance in adults of Rhyzopertha dominica (Coleoptera: Bostrychidae) and Sitophilus oryzae (Coleoptera: Curculionidae)

Degree of dominance of phosphine resistance was investigated in adults of Rhyzopertha dominica F and Sitophilus oryzae L. Efficacy of the grain fumigant phosphine depends on both concentration and exposure period, which raises the possibility that dominance levels vary with exposure period. New and published data were used to test this possibility in adults of R dominica and S oryzae fumigated for periods of up to 144 h. The concentrations required for control of homozygous resistant and susceptible strains and their F1 hybrids decreased with increasing exposure period. For both species the response lines for the homozygous resistant and susceptible strains and their F1 hybrids were parallel. Therefore, neither dominance level nor resistance factor was affected by exposure period. Resistance was incompletely recessive and the level of dominance, calculated at 50% mortality level, was -0.59 for R dominica and -0.65 for S oryzae. The resistant R dominica strain was 30.9 times more resistant than the susceptible strain, compared with 8.9 times for the resistant S oryzae strain. The results suggest that developing discriminating doses for detecting heterozygote adults of either species will be difficult.     

Prevalence of herbicide‐resistant weed species in Malaysian rice fields: A review

The management of weeds in Malaysian rice fields is very much herbicide‐based. The heavy reliance on herbicide for weed control by many rice‐growers arguably eventually has led to the development and evolution of herbicide‐resistant biotypes in Malaysian rice fields over the years. The continuous use of synthetic auxin (phenoxy group) herbicides and acetohydroxyacid synthase‐inhibiting herbicides to control rice weeds was consequential in leading to the emergence and prevalence of resistant weed biotypes. This review discusses the history and confirmed cases and incidence of herbicide‐resistant weeds in Malaysian rice fields. It also reviews the Clearfield Production System and its impact on the evolution of herbicide resistance among rice weed species and biotypes. This review also emphasizes the strategies and management options for herbicide‐resistant rice field weeds within the framework of herbicide‐based integrated weed management. These include the use of optimum tillage practices, certified clean seeds, increased crop competition through high seeding rates, crop rotation, the application of multiple modes of action of herbicides in annual rotations, tank mixtures and sequential applications to enable a broad spectrum of weed control, increase the selective control of noxious weed species in a field and help to delay the resistance evolution by reducing the selection pressure that is forced on those weed populations by a specific herbicidal mode of action.     

Establishment of Lolium species resistant to acetolactate synthase‐inhibiting herbicide in and around grain‐importation ports in Japan

Compared with natural seed dispersal, human‐mediated seed dispersal could spread herbicide resistance genes on a much larger scale. Herbicide‐resistant weed seeds have been reported as contaminants in commercial grain. We investigated the contamination of seeds of Lolium species with target‐site mutations conferring resistance to acetolactate synthase (ALS)‐inhibiting herbicides in wheat imported from the USA, Canada and Australia into Japan. We also investigated the establishment of ALS‐inhibiting herbicide‐resistant Lolium species in 12 seaports in Japan that are major entry points for international commodities. We found herbicide‐resistant Lolium spp. seeds from all classes of wheat samples. Resistant individuals became established at six of eight ports where more than 50 kt of imported wheat is unloaded every year. The establishment of resistant Lolium spp. individuals was common at major grain landing ports. Monitoring over 3 years at one port revealed that the frequency of resistant individuals did not fluctuate between years. Many resistant individuals were distributed in front of the entrance of a fodder company, but a few resistant individuals were found in areas 2 km away from the port. The results indicate that gene flow is rare through pollen or seed movement from resistant plants to peripheral populations. Further extensive and long‐term monitoring is necessary to perform a comprehensive risk assessment of herbicide‐resistant plants entering Japan through major commercial ports.     

Herbicide‐resistant genetically‐modified crop: its risks with an emphasis on gene flow

Herbicide‐resistant genetically‐modified (GM) crops are the most widely cultivated worldwide, representing 78% of GM crops in 1999, followed by insect‐resistant GM crops with Bt gene. Gene flow is the most touching risk arising from GM crops, and is categorized as three types: within species, between species and between GM crop and other organisms. This review shows that gene flow is a reality in the plant kingdom with evolutionary change. Herbicide resistance evolves naturally and spreads dynamically in weeds. One of the most concerning crop in relation to gene flow is Brassica napus, which has a high outcrossing rate and many relative species. In contrast, frequency of gene flow via outcrossing is relatively low in inbreeding cereal crops such as rice, wheat and barley, but published reports have shown that substantial gene flow is possible. Another possible and immediate risk is herbicide‐resistant GM crops becoming volunteer weeds. Dry direct‐seeded rice is one of the most likely crops in this respect. Stacking different resistance genes in a crop would accelerate multiple resistance evolution in weeds. Multiple resistance to three major herbicides has already been observed in oilseed rape cultivation. More efforts must be made for long‐term risk assessment on GM crops in the natural ecosystem. More studies on weed biology and ecology, particularly reproductive processes in weeds, are essential for better understanding of gene flow and systematic management strategy. We hope that this review motivates researchers to analyze data available now, to collect fundamental information on crops and weeds in agro‐ecosystem, and to lead to better risk assessment and management.     

Development of near-isogenic lines and identification of markers linked to auxinic herbicide resistance in wild mustard (Sinapis arvensis L.)

BACKGROUND: Auxinic herbicides are widely used for selective control of many broadleaf weeds, e.g. wild mustard. An auxinic‐herbicide‐resistant wild mustard biotype may offer an excellent model system to elucidate the mechanism of action of these herbicides. Classical genetic analyses demonstrate that the wild mustard auxinic herbicide resistance is determined by a single dominant gene. Availability of near‐isogenic lines (NILs) of wild mustard with auxinic herbicide resistance (R) and herbicide susceptibility (S) will help to study the fitness penalty as well as the precise characterization of this gene. RESULTS: Eight generations of backcrosses were performed, and homozygous auxinic‐herbicide‐resistant and auxinic‐herbicide‐susceptible NILs were identified from BC₈F₃ families. S plants produced significantly more biomass and seed compared with R plants, suggesting that wild mustard auxinic herbicide resistance may result in fitness reduction. It was also found that the serrated margin of the first true leaf was closely linked to auxinic herbicide resistance. Using the introgressed progeny, molecular markers linked to auxinic herbicide resistance were identified, and a genetic map was constructed. CONCLUSION: The fitness penalty associated with the auxinic herbicide resistance gene may explain the relatively slow occurrence and spread of auxinic‐herbicide‐resistant weeds. The detection of the closely linked markers should hasten the identification and characterization of this gene. Copyright © 2012 Society of Chemical Industry     

Selection pressure effects on the proportion and movement of resistance alleles introgressed from wheat in Aegilops cylindrica

In winter wheat in the USA, Aegilops cylindrica is one of the most troublesome weeds, while the pathogen Oculimacula spp. causes foot rot disease. Imazamox‐resistant (IR) and foot rot‐resistant (FR) wheat cultivars represent effective tools to control the weed and prevent disease infection. However, resistance allele (RA) movement between wheat and A. cylindrica facilitates the introgression process under herbicide and disease selection pressure. Field experiments using IR and FR A. cylindrica plants intermixed with susceptible plants were conducted to measure the proportion of the RAs in the progeny and RA movement with and without herbicide and disease selection. Yield components of A. cylindrica plants were determined across treatments. The herbicide RA proportion in the progeny was greater when plants were treated with the herbicide imazamox in both years. Disease RA proportion was greater with disease occurrence only in one year. Herbicide RA movement from resistant to susceptible plants was greater with herbicide than without it only in one year. Plants carrying the RAs had greater total spikelet weight and 1000‐spikelet weight compared with susceptible plants with or without selection. However, susceptible plants produced more spikelets than the resistant ones in the absence of selection. If plants within an A. cylindrica population acquire the herbicide RA, its proportion will increase each generation under selection. These findings contribute to the understanding of crop allele introgression into related species and the evolution of increased weediness, with weed management implications.     

Molecular basis of multiple resistance to ACCase-inhibiting and ALS-inhibiting herbicides in Lolium rigidum

Herbicide resistance in Lolium rigidum is widespread across much of the agricultural land in Australia. As the incidence of herbicide resistance has increased, so has the incidence of multiple herbicide resistance. This reduces the herbicide options available for control of this weed. This study reports on the successful amplification and sequencing of the acetolactate synthase (ALS) gene of L. rigidum using primers designed from sequence information of related taxa. This enables, for the first time, the successful determination of a mutation in the ALS gene of this species that provides resistance to ALS‐inhibiting herbicides. This mutation causes amino acid substitution at Trp574 (numbering standardised to Arabidopsis thaliana) to Leu which had been reported to confer a high level of resistance against all classes of ALS inhibitor herbicides. In addition, multiple resistance to ALS‐inhibiting and acetyl‐coenzyme A carboxylase‐inhibiting herbicides is acquired through the independent accumulation of mutant alleles for the target sites. This may thus explain some of the irregular, mosaic resistance patterns that occur in this predominantly outcrossing species.     

Inheritance of fomesafen and imazethapyr resistance in a multiple herbicide-resistant Euphorbia heterophylla population

Euphorbia heterophylla populations endued with resistance to both imazethapyr (an acetolactate synthase inhibitor) and fomesafen (a protoporphyrinogen oxidase inhibitor) were first detected in Brazil in 2004. The objectives of this study were to determine the number and dominance of genes conferring imazethapyr and fomesafen resistance in E. heterophylla and to establish the types of inheritance of the resistance traits. It was hypothesised that two dominant nuclear genes control this herbicide resistance and each gene confers resistance to a single herbicide. We crossed a susceptible (S) and a multiple-resistant (R) E. heterophylla biotype and generated F₁ families which, in turn, were self-fertilised to produce F₂ families. Backcrosses of the F₁ families with the S- and R parental biotypes resulted in BC_s and BC_r families respectively. The F₁, F₂, BC_s and BC_r families and the S and R parental biotypes were subjected to imazethapyr and fomesafen wherein each herbicide was used as a selecting agent. F₁ plants and the S- and R parental biotypes were used to evaluate the dominance of the resistance trait in multiple-dose bioassays with imazethapyr and fomesafen. The observed frequencies of resistant plants in the F₁, F₂, BC_s and BC_r families did not significantly differ from the expected frequencies for a resistance trait regulated by two dominant genes in which each gene confers resistance to a single herbicide. The lack of difference in herbicide response between the F₁ family and the R parental biotype was taken as evidence for completely dominant resistance to imazethapyr and fomesafen. Herbicide resistance in E. heterophylla presents with dominant monogenic nuclear inheritance for each herbicide mode of action. Our findings underscore the necessity and urgency of adopting integrated strategies to control E. heterophylla and to inhibit the evolution of new herbicide-resistant strains.     

Challenges for herbicide resistance evolution and management: 50 years after Harper

Evolved resistance to herbicides is a classic example of ‘evolution in action’. This paper calls for a greater integration of ‘evolutionary‐thinking’ into herbicide resistance research. This integration, it is argued, should lead weed scientists to become less focused on simply describing resistance and more driven towards a deeper understanding of the evolutionary forces that underpin resistance evolution. I have attempted in this short paper to initiate a debate into how this might be done. In the first instance, I have highlighted the widespread misunderstanding and mis‐measurement by weed scientists of fitness and fitness costs. I have also speculated on the potential for herbicide rotations to exacerbate resistance problems by selecting for generalist (metabolic) resistance. Finally, I have discussed in greater detail the contribution of herbicide rates to resistance evolution and have reported work conducted in Australia which has shown the potential for low herbicide doses to rapidly select for very high levels of resistance in Lolium rigidum. The controversial hypotheses and suggestions put forward need to be tested by field experimentation. They may prove to be unfounded or incorrect, but if they cause us to question and expand the current resistance paradigm they will have been useful.     

The role of fungal endophyte infection in the evolution of Lolium multiflorum resistance to diclofop-methyl

Diclofop-methyl resistance was evaluated in populations of Italian ryegrass ( Lolium multiflorum Lam.) infected and uninfected with fungal endophyte ( Neotyphodium ). Survival was tested in susceptible populations using herbicide screening. The results served as inputs to a model for investigating the role of endophyte infection in the evolution of L. multiflorum resistance to herbicide. The tolerance of infected plants varied depending on the origin of the population and the herbicide dose. Only in some populations and at some diclofop-methyl doses did plants infected with these endophytes have higher survivorship than endophyte-free plants. The model demonstrated that endophytes might indeed play an important role in the evolution of herbicide-resistant weeds, delaying the appearance of herbicide resistance.     

Genetic variation and phylogenetic relationships of triazine-resistant and triazine-susceptible biotypes of Solanum nigrum– analysis using RAPD markers

The expansion of weed species is a major problem in agriculture, especially when the number of herbicide-resistant biotypes is rising continuously. The major ecological questions associated with the evolution of herbicide resistance involve an intricate understanding of the interplay between gene frequency, fitness, inheritance and gene flow. In this study, the RAPD (Random Amplified Polymorphic DNA) technique, which facilitates detection of variability at DNA level, was used to examine the spread of Solanum nigrum L. populations. Twenty-five populations, from Poland, France and the UK, were analysed. Six populations from Poland and one from France showed target site-based triazine resistance. The genetic relationship between individuals was studied using the RAPD technique. It was found that some resistant populations from the Gabin and Grojec areas show very high affinity levels compared with individuals from France. Three groups of populations in which resistance had developed independently were distinguished. The results of the present investigation suggest that migratory birds, such as Turdus pilaris L. and Sturnus vulgaris L., play an important in spreading S. nigrum seeds.     

Herbicide resistance costs: what are we actually measuring and why?

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. © 2017 Society of Chemical Industry