Rapid Evolution Of Herbicide Resistance Research Articles

The Pro-197-Thr mutation in the ALS gene confers novel resistance patterns to ALS-inhibiting herbicides in Bromus japonicus in China.

Bromus japonicus is one of the most notorious agricultural weeds in China. The long-term use of ALS-inhibiting herbicides has led to rapid evolution of herbicide resistance in B. japonicus. B. japonicus population (BJ-R) surviving mesosulfuron-methyl treatment was collected from wheatland. Here, we aimed to confirm the resistance mechanisms in this putative resistant population. The dose-reponse tests were used to test the resistance level of the B. japonicus to ALS-inhibiting herbicides. Pretreatment with P450 and GST inhibitors and GST activity assays were used to determine whether P450 or GST was involved in the resistance of the BJ-R population. Sanger sequencing was used to analyse the ALS mutation of the BJ-R population. RT-qPCR was used to confirm the the expression levels of the ALS gene in mesosulfuron-methyl -resistant (BJ-R) and-susceptible (BJ-S) B. japonicus. An in vitro ALS activity assay was used to determine the ALS activity of the BJ-R and BJ-S populations. Homology modelling and docking were used to determine the binding energy of the BJ-R and BJ-S populations with ALS-inhibiting herbicides. B. japonicus population (BJ-R) was confirmed to be 454- and 2.7-fold resistant to the SU herbicides mesosulfuron-methyl and nicosulfuron, and 7.3-, 2.3-, 1.1- and 10.8-fold resistant to the IMI herbicide imazamox, the TP herbicide penoxsulam, the PTB herbicide pyribenzoxim and the SCT herbicide flucarbazone-sodium, respectively, compared with its susceptible counterpart (BJ-S). Neither a P450 inhibitor nor a GST inhibitor could reverse the level of resistance to mesosulfuron-methyl in BJ-R. In addition, no significant differences in GST activity were found between the BJ-R and BJ-S. ALS gene sequencing revealed a Pro-197-Thr mutation in BJ-R, and the gene expression had no significant differences between the BJ-R and BJ-S. The ALS activity of BJ-R was 106-fold more tolerant to mesosulfuron-methyl than that of BJ-S. Molecular docking showed that the binding energy of the ALS active site and mesosulfuron-methyl was changed from -6.67 to -4.57 kcal mol-1 due to the mutation at position 197. These results suggested that the Pro-197-Thr mutation was the main reason for the high resistance level of BJ-R to mesosulfuron-methyl. Unlike previous reports of the cross-resistance pattern conferred by this mutation, we firstly documented that the Pro-197-Thr mutation confers broad cross-resistance spectrums to ALS-inhibiting herbicides in B. japonicus.

Evolution of Herbicide Resistant Weeds in Agro-ecological Systems

Weed management through herbicides continues to be the most efficient and cost-effective component of integrated weed management (IWM) in crop production systems. However, the current production systems are characterised by intensive, inappropriate use of herbicides along with misapplication which creates selection pressure and leads to the rapid evolution of herbicide resistance in weeds. Currently, there are 511 unique cases of herbicide-resistant weed species globally, involving 266 species and these comprise 153 and 113 dicots and monocots respectively. To date, herbicide resistance has been reported from 96 crops in more than 71 countries. Furthermore, weeds have evolved resistance to 21 of the 31 known sites of herbicide action in different crops. Understanding the mechanisms of herbicide resistance is therefore essential which when coupled with the ecological and management factors that affect herbicide resistance would lead to the development of appropriate, profitable, and sustainable weed management strategies. The review is aimed at the development of herbicide resistance, mechanisms of herbicide resistance, factors that influence the rate of resistance development and management of herbicide resistance by growers.

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Repeated herbicide applications in agricultural fields exert strong selection on weeds such as blackgrass (Alopecurus myosuroides), which is a major threat for temperate climate cereal crops. This inadvertent selection pressure provides an opportunity for investigating the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much target-site resistance (TSR) relies on de novo mutations vs. standing variation is important for developing strategies to manage herbicide resistance. We first generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Next, through empirical data in the form of highly accurate long-read amplicons of alleles encoding acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS) variants, we showed that most populations with resistance due to TSR mutations-23 out of 27 and six out of nine populations for ACCase and ALS, respectively-contained at least two TSR haplotypes, indicating that soft sweeps are the norm. Finally, through forward-in-time simulations, we inferred that TSR is likely to mainly result from standing genetic variation, with only a minor role for de novo mutations.

Emergence pattern of horseweed (Erigeron canadensis L.) accessions across Nebraska

AbstractHorseweed is a North American indigenous plant species commonly found in Nebraska cropping systems. Horseweed management is challenging because of horseweed’s prolific seed production, long-distance seed dispersal via wind, competitiveness, and rapid evolution of herbicide resistance. Understanding the horseweed emergence pattern across Nebraska can contribute to implementing effective and more sustainable tactics to minimize its impact on cropping systems. Field studies were conducted during fall and spring from 2016 to 2018 in Lincoln (corn and soybean), North Platte (wheat stubble and soybean), and Scottsbluff (corn and fallow) to investigate the emergence pattern of horseweed accessions from Lincoln, North Platte, and Scottsbluff, NE. Results show that most horseweed seedling emergence occurred in fall (99%) and only a few seedlings emerged in spring across locations, except in the wheat stubble experiment at North Platte, where higher spring emergence was detected (3% to 22%). In four out of six experiments, the density of total emerged seedlings of each accession was greatest when established in their site of origin. Our results suggest that late fall and/or early spring is likely the best timing for horseweed management across Nebraska.

Application of synthetic auxin herbicides to suppress seed viability of Italian ryegrass (Lolium perenne ssp. multiflorum) in tall fescue seed production

AbstractItalian ryegrass is one of the most troublesome weeds worldwide because of the rapid evolution of herbicide resistance in this species. Oregon tall fescue seed production requires high seed purity, demanding good control of Italian ryegrass. The necessity to control herbicide-resistant Italian ryegrass and maintain tall fescue seed purity created interest in new chemical management options. The objectives of this study were to assess the effects of synthetic auxin herbicides on seed viability of Italian ryegrass biotypes and the feasibility of this management strategy for use in tall fescue seed production. Eight treatments of synthetic auxin herbicides were applied to Italian ryegrass and tall fescue at two growth stages (boot and anthesis): dicamba (1.0 and 2.2 kg ae ha−1), 2,4-D (1.1 and 2.2 kg ae ha−1), aminopyralid (0.5 kg ae ha−1), dicamba + 2.4-D (0.8 + 1.1 kg ae ha−1), 2.4-D + clopyralid (1.1 + 0.3 kg ae ha−1), and halauxifen-methyl + florasulam (0.4 kg ae ha−1 + 0.4 kg ai ha−1). Aminopyralid applied at boot and anthesis stages of Italian ryegrass reduced seed viability. Aminopyralid treatments reduced seed viability and weight of Italian ryegrass more than 50% compared to the control. Four biotypes from different locations in western Oregon with different types of herbicide resistance were sprayed, and differences in aminopyralid effect among Italian ryegrass biotypes were documented. Aminopyralid reduced the speed of germination by 1 to 2 d. Aminopyralid treatments had a greater effect when applied at the anthesis stage and had a greater negative impact on tall fescue. Tall fescue plants were more susceptible to aminopyralid, so this management practice is not feasible for tall fescue seed production. Future studies are needed to understand the physiological mechanisms involved in the reduced seed viability and to define an optimum aminopyralid rate for different Italian ryegrass biotypes.

Effect of PPO-Inhibiting Herbicides on the Growth and Sex Ratio of a Dioecious Weed Species Amaranthus palmeri (Palmer Amaranth)

Amaranthus palmeri S. Watson (Palmer amaranth) is a fast-growing, dioecious, highly competitive agricultural weed species, which is spreading across the US Midwest. Population sex ratios are an important consideration in the management of A. palmeri populations as this species has become resistant to several herbicide sites of action, and there is need to minimize seed production by female plants. Environmental conditions, particularly stressors, may influence sex ratios, and herbicides act as major stressors and evolutionary filters in agricultural fields. Amaranthus spp. have shown a tendency for rapid evolution of herbicide resistance, with the frequency of protoporphyrinogen oxidase (PPO)-inhibitor resistance increasing across the Midwestern US. A greenhouse experiment was conducted to investigate the effect of two PPO-inhibiting herbicide treatments of either lactofen or fomesafen on four different Illinois populations (Cahokia, Collinsville, Rend Lake, and Massac). Plants raised from seed from the Massac population were tallest, and both males and females from this population also had the highest vegetative biomass. Female plants from the Collinsville population had more reproductive biomass than male plants. Control populations were male-biased (Cahokia, Collinsville), female-biased (Masaac), and 1:1 (Rend Lake). Lactofen shifted the male-biased populations to female-biased or 1:1 and the female-biased population to 1:1. Fomesafen-treated populations were male-biased or 1:1. This study suggests that PPO-inhibiting herbicide treatments may influence the growth and sex ratio of A. palmeri populations, which is an underlying factor in the rate of herbicide evolution in this species. An understanding of the underlying mechanisms of how external factors influence sex ratios may eventually provide an opportunity to reduce seed production in populations by shifting sex ratios towards a male bias.

Recurrent Sublethal-Dose Selection for Reduced Susceptibility of Palmer Amaranth (Amaranthus palmeri) to Dicamba

The management of glyphosate-resistant Palmer amaranth has been a challenge in southern United States cropping systems. Registration of dicamba-resistant crops will provide an alternative management option to control herbicide-resistant Palmer amaranth populations, particularly those having resistance to herbicide Groups 2, 3, 5, 9, 14, and 27. However, repeated use of sublethal doses of dicamba may lead to rapid evolution of herbicide resistance, especially in Palmer amaranth—a species with a strong tendency to evolve resistance. Therefore, selection experiments with dicamba were conducted on Palmer amaranth using sublethal doses. In the greenhouse, a known susceptible Palmer amaranth population was subjected to sublethal dicamba doses for three generations (P1–P3). Susceptibility of the individuals to dicamba was evaluated, and its susceptibility to 2,4-D was characterized. Based on the greenhouse study, following three generations of dicamba selection, the dose required to cause 50% mortality increased from 111 g ae ha−1for parental individuals (P0) to 309 g ae ha−1for the P3. Furthermore, reduced susceptibility of the P3to 2,4-D was also evident. This research presents the first evidence that recurrent use of sublethal dicamba doses can lead to reduced susceptibility of Palmer amaranth to dicamba as well as 2,4-D. Here, we show that selection from sublethal dicamba doses has an important role in rapid evolution of Palmer amaranth with reduced susceptibility to auxin-type herbicides.

Palmer Amaranth (Amaranthus palmeri) Identification and Documentation of ALS-Resistance in Argentina

Palmer amaranth has greatly disrupted agricultural practices in the United States with its rapid growth and rapid evolution of herbicide resistance. This weed species is now suspected in Argentina. To document whether the suspected plant populations are indeed Palmer amaranth, molecular comparisons to known standards were conducted. Additionally, these same plant populations were screened for possible herbicide resistance to several acetolactate synthase (ALS)-inhibiting herbicides. Sequencing data confirmed that suspected populations (A2, A3, A4) were indeed Palmer amaranth. Another population (A1) was tested to determine whether hybridization had occurred between Palmer amaranth and mucronate amaranth the native amaranth species of the region. Tests confirmed that no hybridization had occurred and that A1 was simply a unique phenotype of mucronate amaranth. Each population was screened for resistance to imazapic, nicosulfuron, and diclosulam. All Palmer amaranth populations from Argentina were shown to be resistant to at least one ALS-inhibiting herbicide. The populations were then subjected to further testing to identify the mutation responsible for the observed ALS resistance. All mucronate amaranth populations exhibited a mutation previously documented to confer ALS resistance (S653N). No known resistance-conferring mutations were found in Palmer amaranth.

Evolution of Herbicide Resistance in Lolium rigidum under Low Herbicide Rates: An Australian Experience

ABSTRACTRecent studies have shown the potential of lower than recommended herbicide rates to enhance the herbicide resistance level of a troublesome weed, annual ryegrass (Lolium rigidum Gaud.). Rapid evolution of herbicide resistance was possible, because low herbicide rates could select for minor traits and their accumulation through cross‐pollination. These studies are highly relevant for the reason that low herbicide rates prevail in global agriculture—particularly in Australia, where recommended herbicide rates are the lowest in the world. In addition, growers use lower than recommended rates for economic reasons and there is no bio‐regulatory authority to control the use of herbicides. Indeed, low herbicide rate alone would not lead to rapid evolution of herbicide resistance, but its interaction with the genetic and biological potential of a target weed species is also crucial to decide the pace of herbicide resistance evolution. Alarmingly, L. rigidum is genetically highly variable and possesses many biological and genetic attributes that aid this species to augment resistance mechanisms to combat the never‐ending herbicide selection pressure. In this review, the biological and genetic potential of this cross‐pollinating species to evolve as one of the most troublesome weeds is examined. In that way, this review would be a practical lesson to frame future herbicide resistance management strategies for troublesome weeds in global agriculture. A diversified herbicide‐use pattern and integration of appropriate nonchemical methods are envisaged to minimize the pace of herbicide resistance evolution. Another important message is that herbicides should be used only at the recommended rates.

De novo Assembly and Characterization of the Barnyardgrass (Echinochloa crus-galli) Transcriptome Using Next-Generation Pyrosequencing

BackgroundBarnyardgrass (Echinochloa crus-galli) is an important weed that is a menace to rice cultivation and production. Rapid evolution of herbicide resistance in this weed makes it one of the most difficult to manage using herbicides. Since genome-wide sequence data for barnyardgrass is limited, we sequenced the transcriptomes of susceptible and resistant barnyardgrass biotypes using the 454 GS-FLX platform.Results454 pyrosequencing generated 371,281 raw reads with an average length of 341.8 bp, which made a total length of 126.89 Mb (SRX160526). De novo assembly produced 10,142 contigs (∼5.92 Mb) with an average length of 583 bp and 68,940 singletons (∼22.13 Mb) with an average length of 321 bp. About 244,653 GO term assignments to the biological process, cellular component and molecular function categories were obtained. A total of 6,092 contigs and singletons with 2,515 enzyme commission numbers were assigned to 151 predicted KEGG metabolic pathways. Digital abundance analysis using Illumina sequencing identified 78,124 transcripts among susceptible, resistant, herbicide-treated susceptible and herbicide-treated resistant barnyardgrass biotypes. From these analyses, eight herbicide target-site gene groups and four non-target-site gene groups were identified in the resistant biotype. These could be potential candidate genes involved in the herbicide resistance of barnyardgrass and could be used for further functional genomics research. C4 photosynthesis genes including RbcS, RbcL, NADP-me and MDH with complete CDS were identified using PCR and RACE technology.ConclusionsThis is the first large-scale transcriptome sequencing of E. crus-galli performed using the 454 GS-FLX platform. Potential candidate genes involved in the evolution of herbicide resistance were identified from the assembled sequences. This transcriptome data may serve as a reference for further gene expression and functional genomics studies, and will facilitate the study of herbicide resistance at the molecular level in this species as well as other weeds.

Simulation modelling identifies polygenic basis of herbicide resistance in a weed population and predicts rapid evolution of herbicide resistance at low herbicide rates

The potential for low rates of diclofop-methyl to result in rapid evolution of herbicide resistance in a herbicide-susceptible Lolium rigidum (annual ryegrass) population was demonstrated in a recent crop-field study. In this present study, the data from the crop-field study was used together with simulation modelling to identify possible genetics of the herbicide resistance that was selected for. This analysis clearly indicated that the herbicide resistance was polygenic. Subsequently, the estimated genetic possibilities were used to parameterise a model of herbicide resistance evolution in a simulated crop-field situation, and the potential of different rates of diclofop-methyl (ACCase herbicide) to cause herbicide-resistance evolution in L. rigidum was explored and compared using the calibrated model. The calibrated model outputs indicated that the evolution of diclofop-methyl resistance would generally be faster at low herbicide rates than at higher rates due to the rapid selection of minor gene herbicide resistance traits at low rates and their subsequent recombination by cross-pollination. The results of the study therefore indicate potential risks in herbicide rate cutting and highlight the need for careful scientific evaluation of any herbicide use rate for its potential to select for minor gene herbicide resistance from a weed population.

An Herbicide-Susceptible Rigid Ryegrass (Lolium rigidum) Population Made Even More Susceptible

A wild population of a plant species, especially a cross-pollinated species, can display considerable genetic variation. Genetic variability is evident in differential susceptibility to an herbicide because the population can show continuous phenotypic variation. Recent, recurrent selection studies have revealed that phenotypic variation in response to low herbicide rates is heritable and can result in rapid evolution of herbicide resistance in genetically variable cross-pollinated rigid ryegrass. In this study, the heritable genetic variation in an herbicide-susceptible rigid ryegrass population was exploited to shift the population toward greater herbicide susceptibility by recurrent selection. To enhance herbicide susceptibility, herbicide-susceptible rigid ryegrass plants were divided into two identical clones, and one series of cloned plants was treated with a low rate of herbicide (diclofop). The nontreated clones of individuals that did not survive the herbicide treatment were selected and bulk-crossed to obtain the susceptible progeny. After two cycles of selection, the overall susceptibility to diclofop was doubled. The results indicate that minor genes for resistance are present in an herbicide-susceptible rigid ryegrass population, and their exclusion can increase susceptibility to diclofop.

Rapid Evolution of Herbicide Resistance by Low Herbicide Dosages

Herbicide rate cutting is an example of poor use of agrochemicals that can have potential adverse implications due to rapid herbicide resistance evolution. Recent laboratory-level studies have revealed that herbicides at lower-than-recommended rates can result in rapid herbicide resistance evolution in rigid ryegrass populations. However, crop-field-level studies have until now been lacking. In this study, we examined the impact of low rates of diclofop on the evolution of herbicide resistance in a herbicide-susceptible rigid ryegrass population grown either in a field wheat crop or in potted plants maintained in the field. Subsequent dose–response profiles indicated rapid evolution of diclofop resistance in the selected rigid ryegrass lines from both the crop-field and field pot studies. In addition, there was moderate level of resistance in the selected lines against other tested herbicides to which the population has never been exposed. This resistance evolution was possible because low rates of diclofop allowed substantial rigid ryegrass survivors due to the potential in this cross-pollinated species to accumulate all minor herbicide resistance traits present in the population. The practical lesson from this research is that herbicides should be used at the recommended rates that ensure high weed mortality to minimize the likelihood of minor herbicide resistance traits leading to rapid herbicide resistance evolution.

Evolution in Action: Plants Resistant to Herbicides

Modern herbicides make major contributions to global food production by easily removing weeds and substituting for destructive soil cultivation. However, persistent herbicide selection of huge weed numbers across vast areas can result in the rapid evolution of herbicide resistance. Herbicides target specific enzymes, and mutations are selected that confer resistance-endowing amino acid substitutions, decreasing herbicide binding. Where herbicides bind within an enzyme catalytic site very few mutations give resistance while conserving enzyme functionality. Where herbicides bind away from a catalytic site many resistance-endowing mutations may evolve. Increasingly, resistance evolves due to mechanisms limiting herbicide reaching target sites. Especially threatening are herbicide-degrading cytochrome P450 enzymes able to detoxify existing, new, and even herbicides yet to be discovered. Global weed species are accumulating resistance mechanisms, displaying multiple resistance across many herbicides and posing a great challenge to herbicide sustainability in world agriculture. Fascinating genetic issues associated with resistance evolution remain to be investigated, especially the possibility of herbicide stress unleashing epigenetic gene expression. Understanding resistance and building sustainable solutions to herbicide resistance evolution are necessary and worthy challenges.

High survival frequencies at low herbicide use rates in populations of Lolium rigidum result in rapid evolution of herbicide resistance

The frequency of phenotypic resistance to herbicides in previously untreated weed populations and the herbicide dose applied to these populations are key determinants of the dynamics of selection for resistance. In total, 31 Lolium rigidum populations were collected from sites with no previous history of exposure to herbicides and where there was little probability of gene flow from adjacent resistant populations. The mean survival frequency across all 31 populations following two applications of commercial rates (375 g ha(-1)) of the acetyl-coenzyme A carboxylase (ACCase) inhibiting herbicide, diclofop-methyl was 0.43%. Survivors from five of these populations were grown to maturity and seed was collected. Dose-response experiments compared population level resistance to diclofop-methyl in these selected lines with their original parent populations. A single cycle of herbicide selection significantly increased resistance in all populations (LD(50) R:S ratios ranged from 2.8 to 23.2), confirming the inheritance and genetic basis of phenotypic resistance. In vitro assays of ACCase inhibition by diclofop acid indicated that resistance was due to a non-target-site mechanism. Following selection with diclofop-methyl, the five L. rigidum populations exhibited diverse patterns of cross-resistance to ACCase and ALS-inhibiting herbicides, suggesting that different genes or gene combinations were responsible for resistance. The relevance of these results to the management of herbicide resistance are discussed.

Recurrent selection with reduced herbicide rates results in the rapid evolution of herbicide resistance in Lolium rigidum

There has been much debate regarding the potential for reduced rates of herbicide application to accelerate evolution of herbicide resistance. We report a series of experiments that demonstrate the potential for reduced rates of the acetyl-co enzyme A carboxylase (ACCase)-inhibiting herbicide diclofop-methyl to rapidly select for resistance in a susceptible biotype of Lolium rigidum. Thirty-six percent of individuals from the original VLR1 population survived application of 37.5 g diclofop-methyl ha(-1) (10% of the recommended field application rate). These individuals were grown to maturity and bulk-crossed to produce the VLR1 low dose-selected line VLR1 (0.1). Subsequent comparisons of the dose-response characteristics of the original and low dose-selected VLR1 lines demonstrated increased tolerance of diclofop-methyl in the selected line. Two further rounds of selection produced VLR1 lines that were resistant to field-applied rates of diclofop-methyl. The LD50 (diclofop-methyl dose required to cause 50% mortality) of the most resistant line was 56-fold greater than that of the original unselected VLR1 population, indicating very large increases in mean population survival after three cycles of selection. In vitro ACCase inhibition by diclofop acid confirmed that resistance was not due to an insensitive herbicide target-site. Cross-resistance studies showed increases in resistance to four herbicides: fluazifop-P-butyl, haloxyfop-R-methyl, clethodim and imazethapyr. The potential genetic basis of the observed response and implications of reduced herbicide application rates for management of herbicide resistance are discussed.

Evolution of herbicide resistance in weeds: initial frequency of target site-based resistance to acetolactate synthase-inhibiting herbicides in Lolium rigidum.

The frequency of individuals resistant to two acetolactate synthase (ALS)-inhibiting herbicides in three previously untreated populations of Lolium rigidum was determined. The frequency of individuals resistant to the sulfonylurea herbicide sulfometuron-methyl varied from 2.2 x 10(-5) to 1.2 x 10(-4) and the frequency of individuals resistant to the imidazolinone herbicide imazapyr varied from 1 x 10(-5) to 5.8 x 10(-5) depending on the population. Application of sulfometuron-methyl selected individuals with a herbicide-insensitive ALS, which was also cross-resistant to imazapyr. The high initial frequency of individuals resistant to ALS-inhibiting herbicides in L. rigidumpopulations never previously exposed to these herbicides helps explain the rapid evolution of herbicide resistance in this species once ALS-inhibiting herbicides were used.