Enhanced rates of herbicide metabolism in low herbicide-dose selected resistant Lolium rigidum

Two Cytochrome P450s, CYP709B1 and CYP704C1, Play Essential Roles in Metabolism-Based Multiple Herbicide Resistance in American Sloughgrass (Beckmannia syzigachne (Steud.) Fernald)

This study confirmed a field population of American sloughgrass (Beckmannia syzigachne (Steud.) Fernald) that developed simultaneously high levels of resistance (resistance index >10) to three divergent modes of action herbicides: fenoxaprop-P-ethyl, mesosulfuron-methyl, and isoproturon. The resistance phenotype observed in this population was not attributed to target-site alterations; rather, the resistant plants exhibited a significant increase in the activity of cytochrome P450s (P450s) and enhanced metabolism rates for all three herbicides. RNA sequencing revealed significant upregulation of two P450s, CYP709B1 and CYP704C1, in the resistant plants both before and after herbicide treatments. Molecular docking predicted that the homology models of these P450s should exhibit a binding affinity for a range of herbicides. The heterologous expression of the identified P450s in yeast cells indicated improved growth in the presence of all three of the aforementioned herbicides. Collectively, the increased expression of CYP709B1 and CYP704C1 likely contributed to the P450s-mediated enhanced metabolism, thereby conferring multiple herbicide resistance in B. syzigachne.

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.

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.

Lab meets field: Accelerated selection and field monitoring concur that non-target-site-based resistance evolves first in the dicotyledonous, allergenic weed Ambrosia artemisiifolia

Assessing weed capacity to evolve herbicide resistance before resistance occurs in the field is of major interest for chemical weed control. We used herbicide selection followed by controlled crosses to provoke accelerated evolution of resistance to imazamox (imidazolinones) and tribenuron (sulfonyurea), two acetolactate-synthase (ALS) inhibitors targeting Ambrosia artemisiifolia. In natural populations with no herbicide application records, some plants were initially resistant to metsulfuron (sulfonylurea), a cereal herbicide. Non-target-site-based resistance (NTSR) to metsulfuron was substantially increased from these plants within two generations. NTSR to imazamox and/or tribenuron emerged in metsulfuron-selected G1 progenies and was strongly reinforced in G2 progenies selected by imazamox or tribenuron. NTSR to the herbicides assayed was endowed by partly overlapping and partly specific pathways. Herbicide sensitivity bioassays conducted over 62 ALS-inhibitor-sprayed fields identified emerging resistance to imazamox and/or tribenuron in 14 A. artemisiifolia populations. Only NTSR was detected in 13 of these populations. In the last population, NTSR was present together with a mutant, herbicide-resistant ALS allele bearing an Ala-205-Thr substitution. NTSR was thus by far the predominant type of resistance to ALS inhibitors in France. This confirmed accelerated selection results and demonstrated the relevance of this approach to anticipate resistance evolution in a dicotyledonous weed.

Cyhalofop-butyl resistance conferred by a novel Trp-2027-Leu mutation of acetyl-CoA carboxylase and enhanced metabolism in Leptochloa chinensis

BACKGROUND

Chinese sprangletop (Leptochloa chinensis (L.) Nees) is an invasive grass weed severely infesting rice fields across China. In October 2020, a suspected resistant Leptochloa chinensis population HFFD3 that survived the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide cyhalofop-butyl applied at its field-recommended rate was collected from a rice field in Feidong County, Anhui Province, China. This study aimed to determine the resistance profile of HFFD3 to ACCase inhibitors and to investigate its mechanisms of resistance to cyhalofop-butyl.

RESULTS

Single-dose testing confirmed that HFFD3 had evolved resistance to cyhalofop-butyl. Two loci encoding plastidic ACCase were each amplified from the susceptible (S) and resistant (R, HFFD3) individual plants. Target gene sequencing and derived cleaved amplified polymorphic sequence assay revealed all the R plants carried a Trp-2027-Leu substitution in their ACCase1,2 copies. Dose-response bioassays revealed that HFFD3 was highly resistant to cyhalofop-butyl and exhibited cross-resistance to metamifop, fenoxaprop-P-ethyl, quizalofop-P-ethyl, and clethodim. Pre-treatment with piperonyl butoxide and 4-chloro-7-nitrobenzoxadiazole considerably reversed the resistance of the R plants to cyhalofop-butyl, by 23% and 43%, respectively. Liquid chromatography-tandem mass spectrometry analysis suggested the metabolic rates of cyhalofop-butyl were significantly faster in the R than in the S plants.

CONCLUSION

This study confirmed the first case of an arable weed species featuring cross-resistance to ACCase-inhibiting herbicides due to a novel Trp-2027-Leu mutation of ACCase. Target gene mutation and cytochrome P450s- and glutathione-S-transferases-involved enhanced metabolism may have simultaneously participated in the resistance of HFFD3 population to cyhalofop-butyl.

Absorption, translocation, and metabolism of florpyrauxifen-benzyl and cyhalofop-butyl in cyhalofop-butyl-resistant barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.]

Dose-response experiments were conducted to assess the sensitivity of one susceptible and three putative resistant (R1, R2, and R3) barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] biotypes to florpyrauxifen-benzyl and cyhalofop-butyl alone and as a formulated premix. Subsequently, potential resistance mechanisms of the barnyardgrass were evaluated. Based on biomass reduction results, resistant/susceptible ratios were calculated for R1 (7.0-50), R2 (7.0-150), and R3 (18-214) biotypes. Absorption and translocation of [¹⁴C]-florpyrauxifen-benzyl decreased in R1 and R3 biotypes, but not for [¹⁴C]-cyhalofop-butyl. The metabolism of [¹⁴C]-florpyrauxifen-benzyl to [¹⁴C]-florpyrauxifen-acid was >2-fold less in resistant biotypes (9-11%) than in the susceptible biotype (23%). Moreover, the production of [¹⁴C]-florpyrauxifen-acid in susceptible barnyardgrass (not in the R biotypes) increased 3-fold when florpyrauxifen-benzyl and cyhalofop-butyl were applied in mixture compared to florpyrauxifen-benzyl applied alone. The tested barnyardgrass biotypes had no mutation in the Transport Inhibitor Response1, auxin-signaling F-box, and acetyl coenzyme A carboxylase genes. Although further studies on cyhalofop-butyl resistance with respect to analysis of specific metabolites are needed, our findings in this study demonstrates that the evolution of florpyrauxifen-benzyl resistance in multiple resistant barnyardgrass can be related to non-target-site resistance mechanisms reducing absorption and translocation of the herbicide and causing reduced conversion or rapid degradation of florpyrauxifen-acid.

Impact of a Novel W2027L Mutation and Non-Target Site Resistance on Acetyl-CoA Carboxylase-Inhibiting Herbicides in a French Lolium multiflorum Population

Herbicides that inhibit acetyl-CoA carboxylase (ACCase) are among the few remaining options for the post-emergence control of Lolium species in small grain cereal crops. Here, we determined the mechanism of resistance to ACCase herbicides in a Lolium multiflorum population (HGR) from France. A combined biological and molecular approach detected a novel W2027L ACCase mutation that affects aryloxyphenoxypropionate (FOP) but not cyclohexanedione (DIM) or phenylpyraxoline (DEN) subclasses of ACCase herbicides. Both the wild-type tryptophan and mutant leucine 2027-ACCase alleles could be positively detected in a single DNA-based-derived polymorphic amplified cleaved sequence (dPACS) assay that contained the targeted PCR product and a cocktail of two discriminating restriction enzymes. Additionally, we identified three well-characterised I1781L, I2041T, and D2078G ACCase target site resistance mutations as well as non-target site resistance in HGR. The non-target site component endowed high levels of resistance to FOP herbicides whilst partially impacting on the efficacy of pinoxaden and cycloxydim. This study adequately assessed the contribution of the W2027L mutation and non-target site mechanism in conferring resistance to ACCase herbicides in HGR. It also highlights the versatility and robustness of the dPACS method to simultaneously identify different resistance-causing alleles at a single ACCase codon.

Recurrent Selection with Sub-Lethal Doses of Mesotrione Reduces Sensitivity in Amaranthus palmeri

Amaranthus palmeri, ranked as the most prolific and troublesome weed in North America, has evolved resistance to several herbicide sites of action. Repeated use of any one herbicide, especially at lower than recommended doses, can lead to evolution of weed resistance, and, therefore, a better understanding of the process of resistance evolution is essential for the management of A. palmeri and other difficult-to-control weed species. Amaranthus palmeri rapidly developed resistance to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors such as mesotrione. The objective of this study was to test the potential for low-dose applications of mesotrione to select for reduced susceptibility over multiple generations in an A. palmeri population collected from an agricultural field in 2001. F₀ plants from the population were initially treated with sub-lethal mesotrione rates and evaluated for survival three weeks after treatment. All F₀ plants were controlled at the 1× rate (x = 105 g ai ha⁻¹). However, 2.5% of the F₀ plants survived the 0.5× treatment. The recurrent selection process using plants surviving various mesotrione rates was continued until the F₄ generation was reached. Based on the GR₅₀ values, the sensitivity index was determined to be 1.7 for the F₄ generation. Compared to F₀, HPPD gene expression level in the F₃ population increased. Results indicate that after several rounds of recurrent selection, the successive generations of A. palmeri became less responsive to mesotrione, which may explain the reduced sensitivity of this weed to HPPD-inhibiting herbicides. The results have significance in light of the recently released soybean and soon to be released cotton varieties with resistance to HPPD inhibitors.

Cytochrome P450-mediated herbicide metabolism in plants: current understanding and prospects

Cytochrome P450s (P450s) have been at the center of herbicide metabolism research as a result of their ability to endow selectivity in crops and resistance in weeds. In the last 20 years, ≈30 P450s from diverse plant species have been revealed to possess herbicide-metabolizing function, some of which were demonstrated to play a key role in plant herbicide sensitivity. Recent research even demonstrated that some P450s from crops and weeds metabolize numerous herbicides from various chemical backbones, which highlights the importance of P450s in the current agricultural systems. However, due to the enormous number of plant P450s and the complexity of their function, expression and regulation, it remains a challenge to fully explore the potential of P450-mediated herbicide metabolism in crop improvement and herbicide resistance mitigation. Differences in the substrate specificity of each herbicide-metabolizing P450 are now evident. Comparisons of the substrate specificity and protein structures of P450s will be beneficial for the discovery of selective herbicides and may lead to the development of crops with higher herbicide tolerance by transgenics or genome-editing technologies. Furthermore, the knowledge will help design sound management strategies for weed resistance including the prediction of cross-resistance patterns. Overcoming the ambiguity of P450 function in plant xenobiotic pathways will unlock the full potential of this enzyme family in advancing global agriculture and food security. © 2020 Society of Chemical Industry.

Metribuzin resistance via enhanced metabolism in a multiple herbicide resistant Lolium rigidum population

BACKGROUND

The photosystem II (PSII)-inhibiting herbicides are important for Australian farmers to control Lolium rigidum Gaud. and other weed species in trazine tolerant (TT)-canola fields. A L. rigidum population (R) collected from a TT-canola field from Western Australia showed multiple resistance to PSII, acetyl-coenzyme A carboxylase (ACCase) and acetolactate synthase (ALS) inhibitors. The mechanisms of multiple resistance in this R population were determined.

RESULTS

The R population showed a low-level (about 3.0-fold) resistance to the PSII-inhibiting herbicides metribuzin and atrazine. Sequencing of the psbA gene revealed no differences between the R and susceptible (S) sequences. Furthermore, [¹⁴ C]-metribuzin experiments found no significant difference in metribuzin foliar uptake and translocation between the R and S plants. However, [¹⁴ C]-metribuzin metabolism in R plants was 2.3-fold greater than in S plants. The cytochrome P450 monooxygenase inhibitor piperonyl butoxide (PBO) enhanced plant mortality response to metribuzin and atrazine in both R and S populations. In addition, multiple resistance to ALS and ACCase inhibitors are due to known resistance mutations in ALS and ACCase genes.

CONCLUSION

The results demonstrate that enhanced metribuzin metabolism likely involving cytochrome P450 monooxygenase contributes to metribuzin resistance in Lolium rigidum. This is the first report of metabolic resistance to the PSII-inhibiting herbicide metribuzin in Australian Lolium rigidum. © 2020 Society of Chemical Industry.

Cinmethylin controls multiple herbicide-resistant Lolium rigidum and its wheat selectivity is P450-based

BACKGROUND

Multiple-herbicide resistance in Lolium rigidum and other weed species is increasingly exerting pressure on herbicide discovery research for solutions against resistance-prone weeds. In this study we investigate: (i) the responses of L. rigidum populations and wheat to the new herbicide cinmethylin in comparison with other pre-emergence herbicides, (ii) the effect of seed burial depths on cinmethylin efficacy and crop selectivity, and (iii) the basis of cinmethylin selectivity in wheat.

RESULTS

Cinmethylin at 400 g ha^-1 controls herbicide-susceptible and multiple-resistant L. rigidum, with a reduction of >85% in plant emergence and 90% in aboveground biomass. Cinmethylin provides effective control of a large number of field populations of L. rigidum with evident resistance to trifluralin. When the wheat seed is buried ≥1 cm below the cinmethylin-treated soil surface, the emergence of crop seedlings is not different from the untreated control. The organophosphate insecticide phorate synergizes cinmethylin toxicity in wheat, with an LD₅₀ of 682 g ha^-1 in the absence of phorate versus 109 g ha^-1 in the presence of phorate (84% reduction). The synergistic effect of phorate with cinmethylin on herbicide-susceptible L. rigidum appears smaller (a 44% reduction in the LD₅₀ of cinmethylin).

CONCLUSIONS

Cinmethylin is effective in controlling multiple-resistant L. rigidum and appears safe for wheat when the seed is separated at depth from the herbicide applied to the soil surface. The basis of this metabolism-based selectivity is likely regulated by cytochrome P450 monooxygenases. © 2020 Society of Chemical Industry.

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.

Herbicide drift exposure leads to reduced herbicide sensitivity in Amaranthus spp

While the introduction of herbicide tolerant crops provided growers new options to manage weeds, the widespread adoption of these herbicides increased the risk for herbicide spray drift to surrounding vegetation. The impact of herbicide drift in sensitive crops is extensively investigated, whereas scarce information is available on the consequences of herbicide drift in non-target plants. Weeds are often abundant in field margins and ditches surrounding agricultural landscapes. Repeated herbicide drift exposure to weeds could be detrimental to long-term management as numerous weeds evolved herbicide resistance following recurrent-selection with low herbicide rates. The objective of this study was to evaluate if glyphosate, 2,4-D, and dicamba spray drift could select Amaranthus spp. biotypes with reduced herbicide sensitivity. Palmer amaranth and waterhemp populations were recurrently exposed to herbicide drift in a wind tunnel study over two generations. Seeds from survival plants were used for the subsequent rounds of herbicide drift exposure. Progenies were subjected to herbicide dose-response studies following drift selection. Herbicide drift exposure rapidly selected for Amaranthus spp. biotypes with reduced herbicide sensitivity over two generations. Weed management programs should consider strategies to mitigate near-field spray drift and suppress the establishment of resistance-prone weeds on field borders and ditches in agricultural landscapes.

Mechanism of clomazone resistance in Leptochloa fusca spp. fasicularis to clomazone

Bearded sprangletop (Leptochloa fusca spp. fasicularis) is a problematic weed in California rice (Oryza sativa) production. Historically, bearded sprangletop is controlled with clomazone in California rice fields. The continuous use of clomazone and lack of crop rotation in rice fields resulted in resistance to clomazone in several bearded sprangletop. The objective of this research was to determine the clomazone mechanism of resistance of two bearded sprangletop populations in California rice by investigating clomazone absorption, translocation, and metabolism under controlled environmental conditions in two resistant (CRBS1 and CRBS2) and one susceptible (S) populations. Absorption and translocation of ¹⁴C-clomazone were similar in R and S. Clomazone metabolism, as determined by inhibition of cytochrome P450 enzymes with malathion and determining clomazone metabolites profile, was different between S and R 3 days after treatment. Bearded sprangletop pretreated with malathion was 2-fold more sensitive to clomazone than when treated with clomazone alone, suggesting that cytochrome P450-mediated clomazone metabolism might be involved in the mechanism of resistance. An HPLC-MS/MS analysis revealed differences in clomazone metabolism between R and S biotypes. Hydroxymethylclomazone was the most abundant metabolite found in R plants with three and five-fold more abundant in CRBS1 and CRBS2, respectively, when compared to S plants. 5-ketoclomazone, the known toxic metabolite of clomazone, accumulated 2-fold more in S plants than in R plants at 72 h after treatment. This research shows that clomazone is metabolized differently between R and S populations of bearded sprangletop and that P450 monooxidation is likely involved in the mechanism of resistance.

Non-Target-Site Resistance to Herbicides: Recent Developments

Non-target-site resistance (NTSR) to herbicides in weeds can be conferred as a result of the alteration of one or more physiological processes, including herbicide absorption, translocation, sequestration, and metabolism. The mechanisms of NTSR are generally more complex to decipher than target-site resistance (TSR) and can impart cross-resistance to herbicides with different modes of action. Metabolism-based NTSR has been reported in many agriculturally important weeds, although reduced translocation and sequestration of herbicides has also been found in some weeds. This review focuses on summarizing the recent advances in our understanding of the physiological, biochemical, and molecular basis of NTSR mechanisms found in weed species. Further, the importance of examining the co-existence of TSR and NTSR for the same herbicide in the same weed species and influence of environmental conditions in the altering and selection of NTSR is also discussed. Knowledge of the prevalence of NTSR mechanisms and co-existing TSR and NTSR in weeds is crucial for designing sustainable weed management strategies to discourage the further evolution and selection of herbicide resistance in weeds.

10,000-Times Diluted Doses of ACCase-Inhibiting Herbicides Can Permanently Change the Metabolomic Fingerprint of Susceptible Avena fatua L. Plants

Intentional use of low dosage of herbicides has been considered the cause of non-target resistance in weeds. However, herbicide drift could be a source of low dosage that could be detected by weeds and change their metabolism. Furthermore, the minimum dose that a plant can detect in the environment is unknown, and it is unclear whether low doses could modify the response of weeds when they are first exposed to herbicides (priming effects). In this study, we determined the metabolomic fingerprinting using GC-MS of susceptible Avena fatua L. plants exposed to a gradient of doses (1, 0.1, 0.001, 0.0001, and 0x) relative to the recommended dose of clodinafop-propargyl. Additionally, we evaluated the primed plants when they received a second herbicide application. The results showed that even a 10,000-fold dilution of the recommended dose could induce a significant change in the plants’ metabolism and that this change is permanent over the biological cycle. There was no evidence that priming increased its resistance level. However, hormesis increased biomass accumulation and survival in A. fatua plants. Better application methods which prevent herbicide drift should be developed in order to avoid contact with weeds that grow around the crop fields.

Response of Amaranthus spp. following exposure to sublethal herbicide rates via spray particle drift

The adverse consequences of herbicide drift towards sensitive crops have been extensively reported in the literature. However, little to no information is available on the consequences of herbicide drift onto weed species inhabiting boundaries of agricultural fields. Exposure to herbicide drift could be detrimental to long-term weed management as several weed species have evolved herbicide-resistance after recurrent selection with sublethal herbicide rates This study investigated the deposition of glyphosate, 2,4-D, and dicamba spray particle drift from applications with two different nozzles in a low speed wind tunnel, and their impact on growth and development of Amaranthus spp. Herbicide drift resulted in biomass reduction or complete plant mortality. Inflection points (distance to 50% biomass reduction) for Amaranthus tuberculatus were 7.7, 4.0, and 4.1 m downwind distance for glyphosate, 2,4-D, and dicamba applications with the flat-fan nozzle, respectively, whereas these values corresponded to 2.8, 2.5, and 1.9 m for applications with the air-inclusion nozzle. Inflection points for Amaranthus palmeri biomass reduction were 16.3, 10.9, and 11.5 m for glyphosate, 2,4-D, and dicamba applications with the flat-fan nozzle, respectively, whereas these values corresponded to 7.6, 5.4, and 5.4 m for applications with the air-inclusion nozzle. Plants were more sensitive to glyphosate at higher exposure rates than other herbicides, whereas plants were more sensitive to 2,4-D and dicamba at lower exposure rates compared to glyphosate. Applications with the flat-fan nozzle resulted in 32.3 and 11.5% drift of the applied rate at 1.0 and 3.0 m downwind, respectively, whereas the air-inclusion nozzle decreased the dose exposure in the same distances (11.4 and 2.7%, respectively). Herbicide drift towards field boundaries was influenced by nozzle design and exposed weeds to herbicide rates previously reported to select for herbicide-resistant biotypes.

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.

Molecular basis of resistance to ACCase-inhibiting herbicide cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees) from China

Chinese sprangletop (Leptochloa chinensis (L.) Nees) is one of the most troublesome grass weeds in rice in China. Seven suspected cyhalofop-butyl-resistant L. chinensis populations were collected from different rice fields with a history of cyhalofop-butyl use. The level of resistance and resistance mechanisms in seven populations were studied. Dose-response tests indicated that five populations (JS3, JS4, JS6, JS7 and JS8) had evolved high-level resistance (26.9 to 123.0-fold) to cyhalofop-butyl compared with the susceptible (S) population, and other two populations (JS2 and JS5) were still sensitive to the herbicide. Two acetyl-coenzyme A carboxylase (ACCase) genes were cloned from each population, and three different ACCase mutations (Ile-1781-Leu, Trp-1999-Cys, and Trp-2027-Cys) in ACCase2 gene were determined in different resistant (R) populations. In addition, no resistance-conferring mutations was detected in the R population (JS7), and ACCase gene expression was similar between the S and R populations. Thus, non-target-site resistance mechanisms may be involved in the JS7 population. Moreover, the patterns of cross-resistance of JS6 (Ile-1781-Leu), JS4 (Trp-1999-Cys), JS8 (Trp-2027-Cys), and JS7 (unknown resistance mechanisms) populations to other ACCase-inhibiting herbicides were determined. The JS6 and JS8 populations showed resistance to fenoxaprop-P-ethyl, metamifop, clethodim and pinoxaden, the JS4 population was resistant to fenoxaprop-P-ethyl, metamifop and pinoxaden, and the JS7 population had resistance only to fenoxaprop-P-ethyl and metamifop. These results indicated the diversity of the target-site mutations in ACCase gene of L. chinensis, and provide a better understanding of cross-resistance in L. chinensis, which would be helpful for the management of cyhalofop-butyl-resistant L. chinensis.

CYP81A P450s are involved in concomitant cross-resistance to acetolactate synthase and acetyl-CoA carboxylase herbicides in Echinochloa phyllopogon

Californian populations of Echinochloa phyllopogon have evolved multiple-herbicide resistance (MHR), posing a threat to rice production in California. Previously, we identified two CYP81A cytochrome P450 genes whose overexpression is associated with resistance to acetolactate synthase (ALS) inhibitors from two chemical groups. Resistance mechanisms to other herbicides remain unknown. We analyzed the sensitivity of an MHR line to acetyl-CoA carboxylase (ACCase) inhibitors from three chemical groups, followed by an analysis of herbicide metabolism and segregation of resistance of the progenies in sensitive (S) and MHR lines. ACCase herbicide metabolizing function was investigated in the two previously identified P450s. MHR plants exhibited resistance to all the ACCase inhibitors by enhanced herbicide metabolism. Resistance to the ACCase inhibitors segregated in a 3 : 1 ratio in the F₂ generation and completely co-segregated with ALS inhibitor resistance in F₆ lines. Expression of the respective P450 genes conferred resistance to the three herbicides in rice, which is in line with the detection of hydroxylated herbicide metabolites in vivo in transformed yeast. CYP81As are super P450s that metabolize multiple herbicides from five chemical classes, and concurrent overexpression of the P450s induces metabolism-based resistance to the three ACCase inhibitors in MHR E. phyllopogon, as it does to ALS inhibitors.

Tembotrione detoxification in 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor-resistant Palmer amaranth (Amaranthus palmeri S. Wats.)

BACKGROUND

Resistance to the 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicide tembotrione in an Amaranthus palmeri population from Nebraska (NER) has previously been confirmed to be attributable to enhanced metabolism. The objective of this study was to identify and quantify the metabolites formed in Nebraska susceptible (NES) and resistant (NER) biotypes.

RESULTS

NER and NES formed the same metabolites. Tembotrione metabolism in NER differed from that in NES in that resistant plants showed faster 4-hydroxylation followed by glycosylation. The T₅₀ value (time for 50% production of the maximum 4-hydroxylation product) was 4.9 and 11.9 h for NER and NES, respectively. This process is typically catalyzed by cytochrome P450 enzymes. Metabolism differences between NER and NES were most prominent under 28 °C conditions and herbicide application at the four-leaf stage.

CONCLUSION

Further research with the aim of identifying the gene or genes responsible for conferring metabolic resistance to HPPD inhibitors should focus on cytochrome P450s. Such research is important because non-target-site-based resistance (NTSR) poses the threat of cross resistance to other chemical classes of HPPD inhibitors, other herbicide modes of action, or even unknown herbicides. © 2017 Society of Chemical Industry.

Metabolic Pathway of Topramezone in Multiple-Resistant Waterhemp (Amaranthus tuberculatus) Differs From Naturally Tolerant Maize

Waterhemp [Amaranthus tuberculatus (Moq.) Sauer] is a problematic dicot weed in maize, soybean, and cotton production in the United States. Waterhemp has evolved resistance to several commercial herbicides that inhibit the 4-hydroxyphenylpyruvate-dioxygenase (HPPD) enzyme in sensitive dicots, and research to date has shown that HPPD-inhibitor resistance is conferred by rapid oxidative metabolism of the parent compound in resistant populations. Mesotrione and tembotrione (both triketones) have been used exclusively to study HPPD-inhibitor resistance mechanisms in waterhemp and a related species, A. palmeri (S. Wats.), but the commercial HPPD inhibitor topramezone (a pyrazolone) has not been investigated from a mechanistic standpoint despite numerous reports of cross-resistance in the field and greenhouse. The first objective of our research was to determine if two multiple herbicide-resistant (MHR) waterhemp populations (named NEB and SIR) metabolize topramezone more rapidly than two HPPD inhibitor-sensitive waterhemp populations (named SEN and ACR). Our second objective was to determine if initial topramezone metabolite(s) detected in MHR waterhemp are qualitatively different than those formed in maize. An excised leaf assay and whole-plant study investigated initial rates of topramezone metabolism (<24 h) and identified topramezone metabolites at 48 hours after treatment (HAT), respectively, in the four waterhemp populations and maize. Results indicated both MHR waterhemp populations metabolized more topramezone than the sensitive (SEN) population at 6 HAT, while only the SIR population metabolized more topramezone than SEN at 24 HAT. Maize metabolized more topramezone than any waterhemp population at each time point examined. LC-MS analysis of topramezone metabolites at 48 HAT showed maize primarily formed desmethyl and benzoic acid metabolites, as expected based on published reports, whereas SIR formed two putative hydroxylated metabolites. Subsequent LC-MS/MS analyses identified both hydroxytopramezone metabolites in SIR as different hydroxylation products of the isoxazole ring, which were also present in maize 48 HAT but at very low levels. These results indicate that SIR initially metabolizes and detoxifies topramezone in a different manner than tolerant maize.

Perspectives on non-target site mechanisms of herbicide resistance in weedy plant species using evolutionary physiology

Evolutionary physiology merges the disciplines of evolution and physiology, and it is a research approach that has not received much attention for studying the development of herbicide resistance. This paper makes a case for using evolutionary physiology more frequently when studying herbicide resistance, and illustrates this using three areas where more work would be useful: (i) the interaction among major and minor alleles over many generations during the evolution of physiological responses that lead to specific mechanisms of resistance; (ii) the role of epigenetic factors, especially at an early stage of evolution, on the physiological modifications that result in phenotypes that become insensitive to herbicides; and (iii) the interaction between fitness and physiological performance over time, with emphasis on understanding mechanisms that improve the fitness of herbicide-resistant phenotypes during selection.

Investigation of resistance levels and mechanisms to nicosulfuron conferred by non-target-site mechanisms in large crabgrass (Digitaria sanguinalis L.) from China

Large crabgrass is a major grass weed widely distributed across China. This weed infests maize fields and has evolved resistance to the acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron due to continuous and intensive use. In this study, a total of 25 out of 26 large crabgrass populations collected from maize field demonstrated resistance to nicosulfuron. Amino acid modifications in ALS known to confer resistance to ALS-inhibiting herbicides in other weeds, were not found in the 9 tested resistant populations. The P450 inhibitor malathion significantly reversed resistance to nicosulfuron in 3 tested populations, indicating one or more P450s may be involved. Nicosulfuron was metabolized more rapidly in one resistant large crabgrass population than in a susceptible biotype. This demonstrates that the metabolic resistance mechanisms involving one or more P450s may be responsible for large crabgrass resistance to nicosulfuron in this biotype.

Characterisation of glufosinate resistance mechanisms in Eleusine indica

BACKGROUND

An Eleusine indica population has evolved resistance to glufosinate, a major post-emergence herbicide of global agriculture. This population was analysed for target-site (glutamine synthetase) and non-target-site (glufosinate uptake, translocation and metabolism) resistance mechanisms.

RESULTS

Glutamine synthetase (GS) activity extracted from susceptible (S) and resistant (R*) plants was equally sensitive to glufosinate inhibition, with IC₅₀ values of 0.85 mm and 0.99 mm, respectively. The extractable GS activity was also similar in S and R* samples. Foliar uptake of [¹⁴ C]-glufosinate did not differ in S and R* plants, nor did glufosinate net uptake in leaf discs. Translocation of [¹⁴ C]-glufosinate into untreated shoots and roots was also similar in both populations, with 44% to 47% of the herbicide translocated out from the treated leaf 24 h after treatment. The HPLC and LC-MS analysis of glufosinate metabolism revealed no major metabolites in S or R* leaf tissue.

CONCLUSIONS

Glufosinate resistance in this resistant population is not due to an insensitive GS, or increased activity, or altered glufosinate uptake and translocation, or enhanced glufosinate metabolism. Thus, target-site resistance is likely excluded and the exact resistance mechanism(s) remain to be determined. © 2017 Society of Chemical Industry.

Phorate can reverse P450 metabolism-based herbicide resistance in Lolium rigidum

BACKGROUND

Organophosphate insecticides can inhibit specific cytochrome P450 enzymes involved in metabolic herbicide resistance mechanisms, leading to synergistic interactions between the insecticide and the herbicide. In this study we report synergistic versus antagonistic interactions between the organophosphate insecticide phorate and five different herbicides observed in a population of multiple herbicide-resistant Lolium rigidum.

RESULTS

Phorate synergised with three different herbicide modes of action, enhancing the activity of the ALS inhibitor chlorsulfuron (60% LD₅₀ reduction), the VLCFAE inhibitor pyroxasulfone (45% LD₅₀ reduction) and the mitosis inhibitor trifluralin (70% LD₅₀ reduction). Conversely, phorate antagonised the two thiocarbamate herbicides prosulfocarb and triallate with a 12-fold LD₅₀ increase.

CONCLUSION

We report the selective reversal of P450-mediated metabolic multiple resistance to chlorsulfuron and trifluralin in the grass weed L. rigidum by synergistic interaction with the insecticide phorate, and discuss the putative mechanistic basis. This research should encourage diversity in herbicide use patterns for weed control as part of a long-term integrated management effort to reduce the risk of selection of metabolism-based multiple herbicide resistance in L. rigidum. © 2016 Society of Chemical Industry.

Climate change increases the risk of herbicide-resistant weeds due to enhanced detoxification

Global warming will increase the incidence of metabolism-based reduced herbicide efficacy on weeds and, therefore, the risk for evolution of non-target site herbicide resistance. Climate changes affect food security both directly and indirectly. Weeds are the major biotic factor limiting crop production worldwide, and herbicides are the most cost-effective way for weed management. Processes associated with climatic changes, such as elevated temperatures, can strongly affect weed control efficiency. Responses of several grass weed populations to herbicides that inhibit acetyl-CoA carboxylase (ACCase) were examined under different temperature regimes. We characterized the mechanism of temperature-dependent sensitivity and the kinetics of pinoxaden detoxification. The products of pinoxaden detoxification were quantified. Decreased sensitivity to ACCase inhibitors was observed under elevated temperatures. Pre-treatment with the cytochrome-P450 inhibitor malathion supports a non-target site metabolism-based mechanism of herbicide resistance. The first 48 h after herbicide application were crucial for pinoxaden detoxification. The levels of the inactive glucose-conjugated pinoxaden product (M5) were found significantly higher under high- than low-temperature regime. Under high temperature, a rapid elevation in the level of the intermediate metabolite (M4) was found only in pinoxaden-resistant plants. Our results highlight the quantitative nature of non-target-site resistance. To the best of our knowledge, this is the first experimental evidence for temperature-dependent herbicide sensitivity based on metabolic detoxification. These findings suggest an increased risk for the evolution of herbicide-resistant weeds under predicted climatic conditions.

Recurrent selection with reduced 2,4-D amine doses results in the rapid evolution of 2,4-D herbicide resistance in wild radish (Raphanus raphanistrum L.)

BACKGROUND

When used at effective doses, weed resistance to auxinic herbicides has been slow to evolve when compared with other modes of action. Here we report the evolutionary response of a herbicide-susceptible population of wild radish (Raphanus raphanistrum L.) and confirm that sublethal doses of 2,4-dichlorophenoxyacetic acid (2,4-D) amine can lead to the rapid evolution of 2,4-D resistance and cross-resistance to acetolactate synthase (ALS)-inhibiting herbicides.

RESULTS

Following four generations of 2,4-D selection, the progeny of a herbicide-susceptible wild radish population evolved 2,4-D resistance, increasing the LD₅₀ from 16 to 138 g ha^-1 . Along with 2,4-D resistance, cross-resistance to the ALS-inhibiting herbicides metosulam (4.0-fold) and chlorsulfuron (4.5-fold) was evident. Pretreatment of the 2,4-D-selected population with the cytochrome P450 inhibitor malathion restored chlorsulfuron to full efficacy, indicating that cross-resistance to chlorsulfuron was likely due to P450-catalysed enhanced rates of herbicide metabolism.

CONCLUSION

This study is the first to confirm the rapid evolution of auxinic herbicide resistance through the use of low doses of 2,4-D and serves as a reminder that 2,4-D must always be used at highly effective doses. With the introduction of transgenic auxinic-herbicide-resistant crops in the Americas, there will be a marked increase in auxinic herbicide use and therefore the risk of resistance evolution. Auxinic herbicides should be used only at effective doses and with diversity if resistance is to remain a minimal issue. © 2016 Society of Chemical Industry.

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.

Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.)

Background

Flixweed (Descurainia sophia L.) is a troublesome and widespread broadleaf weed in winter fields in China, and has evolved high level resistance to acetolactate synthase (ALS)-inhibiting sulfonylurea herbicide tribenuron-methyl.

Results

We identified a resistant flixweed population (N11) exhibiting 116.3-fold resistance to tribenuron-methyl relative to the susceptible population (SD8). Target-site ALS gene mutation Pro-197-Thr was identified in resistant plants. Moreover, the resistance can be reversed to 28.7-fold by the cytochrome P450 inhibitor malathion. The RNA-Sequencing was employed to identify candidate genes involved in non-target-site metabolic resistance in this population. Total 26 differentially expressed contigs were identified and eight of them (four P450s, one ABC transporter, three glycosyltransferase) verified by qRT-PCR. Consistent over-expression of the two contigs homology to CYP96A13 and ABCC1 transporter, respectively, were further qRT-PCR validated using additional plants from the resistant and susceptible populations.

Conclusions

Tribenuron-methyl resistance in flixweed is controlled by target-site ALS mutation and non-target-site based mechanisms. Two genes, CYP96A13 and ABCC1 transporter, could play an important role in metabolic resistance to tribenuron-methyl in the resistant flixweed population and justify further functional studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2915-8) contains supplementary material, which is available to authorized users.

Genetics of metabolic resistance

Herbicide resistance has become a major issue for many weeds. Metabolic resistance refers to the biochemical processes within organisms that degrade herbicides to less toxic compounds, resulting in a shift of the dose response curve. This type of resistance involves polygenic inheritance. A model is presented linking the biochemical pathway of amino acid synthesis and the detoxifying pathway of an inhibitor of the key enzyme ALS. From this model, resistance factors for each biotype are derived, which are then applied to a polygenic population genetic model for an annual weed plant. Polygenic inheritance is described by a new approach based on tensor products of heredity matrices. Important results from the model are that low dose regimes favour fast emergence of resistant biotypes and that the emergence of resistant biotypes occurs as abrupt outbreaks. The model is used to evaluate strategies for the management of metabolic resistance.

Response to low-dose herbicide selection in self-pollinated Avena fatua

BACKGROUND

When applied at the correct plant stage and dose, herbicides are highly toxic to plants. At reduced, low herbicide doses (below the recommended dose) plants can survive and display continuous and quantitative variation in dose-survival responses. Recurrent (directional) selection studies can reveal whether such a phenotypic variation in plant survival response to low herbicide dose is heritable and leads to herbicide resistance. In a common experimental garden study, we have subjected a susceptible population of self-pollinated hexaploid Avena fatua to low-dose recurrent selection with the ACCase-inhibiting herbicide diclofop-methyl for three consecutive generations.

RESULTS

Significant differences in response to low-dose diclofop-methyl selection were observed between the selected progenies and parent plants, with a twofold diclofop-methyl resistance and cross-resistance to ALS-inhibiting herbicides. Thus, the capacity of self-pollinated A. fatua to respond to low-dose herbicide selection is marginal, and it is much lower than in cross-pollinated L. rigidum. Lolium rigidum in the same experiment evolved 40-fold diclofop-methyl resistance by progressive enrichment of quantitative resistance-endowing traits.

CONCLUSION

Cross-pollination rate, genetic variation and ploidy levels are identified as possible drivers affecting the contrasting capacity of Avena versus Lolium plants to respond to herbicide selection and the subsequent likelihood of resistance evolution at low herbicide dose usage.

Widespread occurrence of both metabolic and target-site herbicide resistance mechanisms in Lolium rigidum populations

BACKGROUND

Lolium rigidum populations in Australia and globally have demonstrated rapid and widespread evolution of resistance to acetyl coenzyme A carboxylase (ACCase)-inhibiting and acetolactate synthase (ALS)-inhibiting herbicides. Thirty-three resistant L. rigidum populations, randomly collected from crop fields in a most recent resistance survey, were analysed for non-target-site diclofop metabolism and all known target-site ACCase gene resistance-endowing mutations.

RESULTS

The HPLC profile of [(14) C]-diclofop-methyl in vivo metabolism revealed that 79% of these resistant L. rigidum populations showed enhanced capacity for diclofop acid metabolism (metabolic resistance). ACCase gene sequencing identified that 91% of the populations contain plants with ACCase resistance mutation(s). Importantly, 70% of the populations exhibit both non-target-site metabolic resistance and target-site ACCase mutations.

CONCLUSIONS

This work demonstrates that metabolic herbicide resistance is commonly occurring in L. rigidum, and coevolution of both metabolic resistance and target-site resistance is an evolutionary reality. Metabolic herbicide resistance can potentially endow resistance to many herbicides and poses a threat to herbicide sustainability and thus crop production, calling for major research and management efforts.

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.

Molecular basis of resistance to imazethapyr in redroot pigweed (Amaranthus retroflexus L.) populations from China

Three putative resistant Amaranthus retroflexus L. populations were collected in Heilongjiang province in China. Whole plant bioassays indicated high resistance (RI > 10) to imazethapyr in the three populations. In vitro acetolactate synthase (ALS) assays revealed that ALS from populations H3, H17 and H39 was less sensitive to imazethapyr inhibition compared to the susceptible population H76. The half-maximal inhibitory concentration (I50) values for H3, H17 and H39 were 14.83, 15.27 and 268 times greater, respectively, than that of the susceptible population H76. Three nucleotide mutations resulted in three known resistance-endowing amino acid substitutions, Ala-205-Val, Trp-574-Leu and Ser-653-Thr in the three resistant populations respectively. Therefore, ALS target-site mutations in resistant A. retroflexus could be responsible for imazethapyr resistance.

Evolution of herbicide resistance mechanisms in grass weeds

Herbicide resistant weeds are becoming increasingly common, threatening global food security. Here, we present BrIFAR: a new model system for the functional study of mechanisms of herbicide resistance in grass weeds. We have developed a large collection of Brachypodium accessions, the BrI collection, representing a wide range of habitats. Wide screening of the responses of the accessions to four major herbicide groups (PSII, ACCase, ALS/AHAS and EPSPS inhibitors) identified 28 herbicide-resistance candidate accessions. Target-site resistance to PSII inhibitors was found in accessions collected from habitats with a known history of herbicide applications. An amino acid substitution in the psbA gene (serine264 to glycine) conferred resistance and also significantly affected the flowering and shoot dry weight of the resistant accession, as compared to the sensitive accession. Non-target site resistance to ACCase inhibitors was found in accessions collected from habitats with a history of herbicide application and from a nature reserve. In-vitro enzyme activity tests and responses following pre-treatment with malathion (a cytochrome-P450 inhibitor) indicated sensitivity at the enzyme level, and give strong support to diclofop-methyl and pinoxaden enhanced detoxification as NTS resistance mechanism. BrIFAR can promote better understanding of the evolution of mechanisms of herbicide resistance and aid the implementation of integrative management approaches for sustainable agriculture.

Metabolism-based herbicide resistance and cross-resistance in crop weeds: a threat to herbicide sustainability and global crop production

Weedy plant species that have evolved resistance to herbicides due to enhanced metabolic capacity to detoxify herbicides (metabolic resistance) are a major issue. Metabolic herbicide resistance in weedy plant species first became evident in the 1980s in Australia (in Lolium rigidum) and the United Kingdom (in Alopecurus myosuroides) and is now increasingly recognized in several crop-weed species as a looming threat to herbicide sustainability and thus world crop production. Metabolic resistance often confers resistance to herbicides of different chemical groups and sites of action and can extend to new herbicide(s). Cytochrome P450 monooxygenase, glycosyl transferase, and glutathione S-transferase are often implicated in herbicide metabolic resistance. However, precise biochemical and molecular genetic elucidation of metabolic resistance had been stalled until recently. Complex cytochrome P450 superfamilies, high genetic diversity in metabolic resistant weedy plant species (especially cross-pollinated species), and the complexity of genetic control of metabolic resistance have all been barriers to advances in understanding metabolic herbicide resistance. However, next-generation sequencing technologies and transcriptome-wide gene expression profiling are now revealing the genes endowing metabolic herbicide resistance in plants. This Update presents an historical review to current understanding of metabolic herbicide resistance evolution in weedy plant species.

Resistance to AHAS inhibitor herbicides: current understanding

Acetohydroxyacid synthase (AHAS) inhibitor herbicides currently comprise the largest site-of-action group (with 54 active ingredients across five chemical groups) and have been widely used in world agriculture since they were first introduced in 1982. Resistance evolution in weeds to AHAS inhibitors has been rapid and identified in populations of many weed species. Often, evolved resistance is associated with point mutations in the target AHAS gene; however non-target-site enhanced herbicide metabolism occurs as well. Many AHAS gene resistance mutations can occur and be rapidly enriched owing to a high initial resistance gene frequency, simple and dominant genetic inheritance and lack of major fitness cost of the resistance alleles. Major advances in the elucidation of the crystal structure of the AHAS (Arabidopsis thaliana) catalytic subunit in complex with various AHAS inhibitor herbicides have greatly improved current understanding of the detailed molecular interactions between AHAS, cofactors and herbicides. Compared with target-site resistance, non-target-site resistance to AHAS inhibitor herbicides is less studied and hence less understood. In a few well-studied cases, non-target-site resistance is due to enhanced rates of herbicide metabolism (metabolic resistance), mimicking that occurring in tolerant crop species and often involving cytochrome P450 monooxygenases. However, the specific herbicide-metabolising, resistance-endowing genes are yet to be identified in resistant weed species. The current state of mechanistic understanding of AHAS inhibitor herbicide resistance is reviewed, and outstanding research issues are outlined.

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.

RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum

Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism-based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA-Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop-resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant-only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up-regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2 -R from F2 -S individuals. In a physiological validation experiment in which 2,4-D pre-treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field-evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance.

Enhanced herbicide metabolism induced by 2,4-D in herbicide susceptible Lolium rigidum provides protection against diclofop-methyl

BACKGROUND

The auxinic herbicide 2,4-D amine is known, in vitro, as a cytochrome P450 inducer. The current study uses 2,4-D pre-treatment, at the whole plant level, to study mechanism(s) of non-target site based herbicide resistance to the ACCase-inhibiting herbicide diclofop-methyl in Lolium rigidum.

RESULTS

The 2,4-D pre-treatment caused up to 10-fold shift in LD50 and GR50 in dose-response to subsequently applied diclofop-methyl in a herbicide susceptible L. rigidum population. Foliar uptake and translocation of (14) C-diclofop-methyl did not differ in 2,4-D pre-treated versus untreated plants. HPLC analysis revealed that de-esterification of diclofop-methyl to toxic diclofop acid was similar, but further metabolism of diclofop acid to non-toxic metabolites was significantly (1.8-fold) faster in 2,4-D pre-treated than untreated plants. HPLC profile of major polar metabolites was similar when L. rigidum and diclofop-methyl tolerant wheat were compared, but wheat metabolised diclofop acid three-fold faster than L. rigidum. In addition, 2,4-D pre-treatment also induced cross-protection against the ALS-inhibiting herbicide chlorsulfuron, and the known P450 inhibitor malathion can reverse this effect.

CONCLUSIONS

Protection against diclofop-methyl provided by 2,4-D pre-treatment in susceptible L. rigidum is associated with higher rates of herbicide metabolism, mirroring that identified in field-evolved, non-target site-based diclofop-methyl resistant populations. 2,4-D may induce higher level expression of herbicide-metabolising genes hence providing protection, and therefore, this 2,4-D induction system can be used, in combination with other genomic approaches, to assist isolating cytochrome P450 and other genes that are involved in herbicide metabolism and endow herbicide resistance in L. rigidum.