Non-Target-Site Resistance to Herbicides: Recent Developments

A novel mutation Trp-2027-Gly in acetyl-CoA carboxylase confers resistance to cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis)

BACKGROUND

Chinese sprangletop [Leptochloa chinensis (L.) Nees] control is threatened by resistance to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. In this study, a L. chinensis population, HFLJ18, that survived cyhalofop-butyl [aryloxyphenoxypropionate (APP) herbicide, CyB] treatment was collected from a rice field in Lujiang County, Anhui Province, China. This study aimed to evaluate the susceptibility of HFLJ18 to herbicides with different modes-of-action and investigate the potential mechanisms of resistance to CyB.

RESULTS

The HFLJ18 population exhibited high levels of resistance to CyB (10.92-fold) and showed resistance to the ACCase inhibitors metamifop (4.63-fold) and fenoxaprop-P-ethyl (8.39-fold), but was susceptible to clethodim, pinoxaden, florpyrauxifen-benzyl, oxadiazon and pretilachlor. Target gene sequencing revealed a novel Trp-to-Gly substitution at codon position 2027 of ACCase in the resistant plants. Molecular docking revealed that the spatial structure of ACCase changed significantly following the substitution, as indicated by reduced H-bonds. A newly derived cleaved amplified polymorphic sequence (dCAPS) marker was subsequently developed to detect the Trp-2027-Gly mutation in the ACCase of L. chinensis. Additionally, pretreatment with the cytochrome P450 (P450) inhibitor piperonyl butoxide (PBO) and the glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) did not reverse resistance to CyB, suggesting that nontarget-site resistance mechanisms were not involved in CyB resistance in the HFLJ18 population.

CONCLUSION

Overall, the resistance to CyB in the HFLJ18 population derived from the mutation of ACCase gene, and to the best of our knowledge, this is the first report of the ACCase Trp-2027-Gly mutation conferring resistance to ACCase-inhibiting herbicides in grass species. © 2024 Society of Chemical Industry.

Confirmation and characterization of the first case of acetolactate synthase (ALS)-inhibitor resistance in Japanese brome (Bromus japonicus) in the US

BACKGROUND

Japanese brome (Bromus japonicus Thumb.) is one of the problematic annual weeds in winter wheat (Triticum aestivum L.) and is generally controlled by acetolactate synthase (ALS) inhibitors. Repeated use of the ALS inhibitor propoxycarbazone-Na resulted in the evolution of resistance to this herbicide in three B. japonicus populations, i.e., R1, R2, and R3 in Kansas (KS). However, the level of resistance and mechanism conferring resistance in these populations is unknown. The objectives of this research were to (i) evaluate the level of resistance to propoxycarbazone-Na in R1, R2, and R3 in comparison with a known susceptible population (S1), (ii) investigate the mechanism of resistance involved in conferring ALS-inhibitor resistance, and (iii) investigate the cross-resistance to other ALS inhibitors.

RESULTS

Dose-response (0 to 16x; x = 44 g ai ha-1 of propoxycarbazone-Na) assay indicated 167, 125, and 667-fold resistance in R1, R2 and R3 populations, respectively, compared to S1 population. ALS gene sequencing confirmed the mutations resulting in amino acid substitutions, i.e., Pro-197-Thr (R3, R1)/Ser (R2, R1) bestowing resistance to these ALS inhibitors. Such amino acid substitutions also showed differential cross-resistance to sulfosulfuron, mesosulfuron-methyl, pyroxsulam, and imazamox among resistant populations. Pretreatment with malathion (a cytochrome P450 enzyme-inhibitor) followed by imazamox treatment suggested cross-resistance to this herbicide possibly via metabolism only in R3 population.

CONCLUSION

Overall, these results confirm the first case of target-site based resistance to ALS inhibitors in B. japonicus in the US, highlighting the need for exploring herbicides with alternative modes of action to enhance weed control in winter wheat. © 2024 Society of Chemical Industry.

Cytochrome P450 CYP81A104 in Eleusine indica confers resistance to multiherbicide with different modes of action

BACKGROUND

Developing herbicide-resistant (HR) crop cultivars is an efficient way to control weeds and minimize crop yield losses. However, widespread and long-term herbicide application has led to the evolution of resistant weeds. Here, we established a resistant (R) E. indica population, collected from imidazolinone-resistant rice cultivar fields.

RESULTS

The R population evolved 4.5-fold resistance to imazamox. Acetolactate synthase (ALS) gene sequencing and ALS activity assays excluded the effect of target-site resistance in this population. P450 inhibitor malathion pretreatment significantly reversed resistance to imazamox. RNA sequencing showed that a P450 gene CYP81A104 was expressed higher in R versus susceptible (S) plants. Arabidopsis overexpressing CYP81A104 showed resistance to ALS inhibitors (imazamox, tribenuron-methyl, penoxsulam and flucarbazone-sodium), PSII inhibitor (bentazone), hydroxyphenyl pyruvate dioxygenase inhibitor (mesotrione) and auxin mimics (MCPA), which was generally consistent with the results presented in the R population.

CONCLUSION

This study confirmed that the CYP81A104 gene endowed resistance to multiherbicides with different modes-of-action. Our findings provide an insight into the molecular characteristics of resistance and contribute to formulating an appropriate strategy for weed management in HR crops. © 2024 Society of Chemical Industry.

Mapping of flumioxazin tolerance in a snap bean diversity panel leads to the discovery of a master genomic region controlling multiple stress resistance genes

Introduction

Effective weed management tools are crucial for maintaining the profitable production of snap bean (Phaseolus vulgaris L.). Preemergence herbicides help the crop to gain a size advantage over the weeds, but the few preemergence herbicides registered in snap bean have poor waterhemp (Amaranthus tuberculatus) control, a major pest in snap bean production. Waterhemp and other difficult-to-control weeds can be managed by flumioxazin, an herbicide that inhibits protoporphyrinogen oxidase (PPO). However, there is limited knowledge about crop tolerance to this herbicide. We aimed to quantify the degree of snap bean tolerance to flumioxazin and explore the underlying mechanisms.

Methods

We investigated the genetic basis of herbicide tolerance using genome-wide association mapping approach utilizing field-collected data from a snap bean diversity panel, combined with gene expression data of cultivars with contrasting response. The response to a preemergence application of flumioxazin was measured by assessing plant population density and shoot biomass variables.

Results

Snap bean tolerance to flumioxazin is associated with a single genomic location in chromosome 02. Tolerance is influenced by several factors, including those that are indirectly affected by seed size/weight and those that directly impact the herbicide's metabolism and protect the cell from reactive oxygen species-induced damage. Transcriptional profiling and co-expression network analysis identified biological pathways likely involved in flumioxazin tolerance, including oxidoreductase processes and programmed cell death. Transcriptional regulation of genes involved in those processes is possibly orchestrated by a transcription factor located in the region identified in the GWAS analysis. Several entries belonging to the Romano class, including Bush Romano 350, Roma II, and Romano Purpiat presented high levels of tolerance in this study. The alleles identified in the diversity panel that condition snap bean tolerance to flumioxazin shed light on a novel mechanism of herbicide tolerance and can be used in crop improvement.

Metabolism-Based Nontarget-Site Mechanism Is the Main Cause of a Four-Way Resistance in Shortawn Foxtail (Alopecurus aequalis Sobol.)

Alopecurus aequalis Sobol. is a predominant grass weed in Chinese winter wheat fields, posing a substantial threat to crop production owing to its escalating herbicide resistance. This study documented the initial instance of an A. aequalis population (AHFT-3) manifesting resistance to multiple herbicides targeting four distinct sites: acetyl-CoA carboxylase (ACCase), acetolactate synthase, photosystem II, and 1-deoxy-d-xylulose-5-phosphate synthase. AHFT-3 carried an Asp-to-Gly mutation at codon 2078 of ACCase, with no mutations in the remaining three herbicide target genes, and exhibited no overexpression of any target gene. Compared with the susceptible population AHFY-3, AHFT-3 metabolized mesosulfuron-methyl, isoproturon, and bixlozone faster. The inhibition and comparison of herbicide-detoxifying enzyme activities indicated the participation of cytochrome P450s in the resistance to all four herbicides, with glutathione S-transferases specifically linked to mesosulfuron-methyl. Three CYP72As and a Tau class glutathione S-transferase, markedly upregulated in resistant plants, potentially played pivotal roles in the multiple-herbicide-resistance phenotype.

Automatic Localization of Soybean Seedlings Based on Crop Signaling and Multi-View Imaging

Soybean is grown worldwide for its high protein and oil content. Weeds compete fiercely for resources, which affects soybean yields. Because of the progressive enhancement of weed resistance to herbicides and the quickly increasing cost of manual weeding, mechanical weed control is becoming the preferred method of weed control. Mechanical weed control finds it difficult to remove intra-row weeds due to the lack of rapid and precise weed/soybean detection and location technology. Rhodamine B (Rh-B) is a systemic crop compound that can be absorbed by soybeans which fluoresces under a specific excitation light. The purpose of this study is to combine systemic crop compounds and computer vision technology for the identification and localization of soybeans in the field. The fluorescence distribution properties of systemic crop compounds in soybeans and their effects on plant growth were explored. The fluorescence was mainly concentrated in soybean cotyledons treated with Rh-B. After a comparison of soybean seedlings treated with nine groups of rhodamine B solutions at different concentrations ranging from 0 to 1440 ppm, the soybeans treated with 180 ppm Rh-B for 24 h received the recommended dosage, resulting in significant fluorescence that did not affect crop growth. Increasing the Rh-B solutions reduced crop biomass, while prolonged treatment times reduced seed germination. The fluorescence produced lasted for 20 days, ensuring a stable signal in the early stages of growth. Additionally, a precise inter-row soybean plant location system based on a fluorescence imaging system with a 96.7% identification accuracy, determined on 300 datasets, was proposed. This article further confirms the potential of crop signaling technology to assist machines in achieving crop identification and localization in the field.

Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy

The increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.

Pro197Ser and the new Trp574Leu mutations together with enhanced metabolism contribute to cross-resistance to ALS inhibiting herbicides in Sinapis alba

White mustard, (Sinapis alba), a problematic broadleaf weed in many Mediterranean countries in arable fields has been detected as resistant to tribenuron-methyl in Tunisia. Greenhouse and laboratory studies were conducted to characterize Target-Site Resistance (TSR) and the Non-Target Site Resistance (NTSR) mechanisms in two suspected white mustard biotypes. Herbicide dose-response experiments confirmed that the two S. alba biotypes were resistant to four dissimilar acetolactate synthase (ALS)-pinhibiting herbicide chemistries indicating the presence of cross-resistance mechanisms. The highest resistance factor (>144) was attributed to tribenuron-methyl herbicide and both R populations survived up to 64-fold the recommended field dose (18.7 g ai ha-1). In this study, the metabolism experiments with malathion (a cytochrome P450 inhibitor) showed that malathion reduced resistance to tribenuron-methyl and imazamox in both populations, indicating that P450 may be involved in the resistance. Sequence analysis of the ALS gene detected target site mutations in the two R biotypes, with amino acid substitutions Trp574Leu, the first report for the species, and Pro197Ser. Molecular docking analysis showed that ALSPro197Ser enzyme cannot properly bind to tribenuron-methyl's aromatic ring due to a reduction in the number of hydrogen bonds, while imazamox can still bind. However, Trp574Leu can weaken the binding affinity between the mutated ALS enzyme and both herbicides with the loss of crucial interactions. This investigation provides substantial evidence for the risk of evolving multiple resistance in S. alba to auxin herbicides while deciphering the TSR and NTSR mechanisms conferring cross resistance to ALS inhibitors.

Genetic Mechanism of Non-Targeted-Site Resistance to Diquat in Spirodela polyrhiza

Understanding non-target-site resistance (NTSR) to herbicides represents a pressing challenge as NTSR is widespread in many weeds. Using giant duckweed (Spirodela polyrhiza) as a model, we systematically investigated genetic and molecular mechanisms of diquat resistance, which can only be achieved via NTSR. Quantifying the diquat resistance of 138 genotypes, we revealed an 8.5-fold difference in resistance levels between the most resistant and most susceptible genotypes. Further experiments suggested that diquat uptake and antioxidant-related processes jointly contributed to diquat resistance in S. polyrhiza. Using a genome-wide association approach, we identified several candidate genes, including a homolog of dienelactone hydrolase, that are associated with diquat resistance in S. polyrhiza. Together, these results provide new insights into the mechanisms and evolution of NTSR in plants.

Fenoxaprop-P-ethyl, mesosulfuron-ethyl, and isoproturon resistance status in Beckmannia syzigachne from wheat fields across Anhui Province, China

Severe infestations of American sloughgrass (Beckmannia syzigachne (Steud.) Fernald) in wheat fields throughout Anhui Province, China, pose a significant threat to local agricultural production. This study aims to evaluate the susceptibility of 37 B. syzigachne populations collected from diverse wheat fields in Anhui Province to three commonly used herbicides: fenoxaprop-P-ethyl, mesosulfuron-ethyl, and isoproturon. Single-dose testing revealed that out of the 37 populations, 31, 26, and 11 populations had either evolved or were evolving resistance to fenoxaprop-P-ethyl, mesosulfuron-ethyl, and isoproturon, respectively. Among them, 25 populations displayed concurrent resistance to both fenoxaprop-P-ethyl and mesosulfuron-ethyl, while eight exhibited resistance to all three tested herbicides. Whole-plant bioassays confirmed that approximately 84% of the fenoxaprop-P-ethyl-resistant populations manifested high-level resistance (resistance index (RI) ≥10); 62% of the mesosulfuron-ethyl-resistant populations and 82% of the isoproturon-resistant populations exhibited low- to moderate-level resistance (2 ≤ RI <10). Three distinct target-site mutations were identified in 27% of fenoxaprop-P-ethyl-resistant populations, with no known resistance mutations detected in the remaining herbicide-resistant populations. The inhibition of cytochrome P450s (P450s) and/or glutathione S-transferases (GSTs) substantially increased susceptibility in the majority of resistant populations lacking mutations at the herbicide target site. In conclusion, resistance to fenoxaprop-P-ethyl and mesosulfuron-ethyl was widespread in B. syzigachne within Anhui Province's wheat fields, while resistance to isoproturon was rapidly evolving due to its escalating usage. Target-site mutations were present in approximately one-third of fenoxaprop-P-ethyl-resistant populations, and alternative mechanisms involving P450s and/or GSTs could explain the resistance observed in most of the remaining populations.

Target-site and non-target-site based resistance to clodinafop-propargyl in wild oats (Avena fatua L.)

Wild oat (Avena fatua L.) is a common and problematic weed in wheat fields in China. In recent years, farmers found it increasingly difficult to control A. fatua using acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. The purpose of this study was to identify the molecular basis of clodinafop-propargyl resistance in A. fatua. In comparison to the S1496 population, whole dose response studies revealed that the R1623 and R1625 populations were 71.71- and 67.76-fold resistant to clodinafop-propargyl, respectively. The two resistant A. fatua populations displayed high resistance to fenoxaprop-p-ethyl (APP) and low resistance to clethodim (CHD) and pinoxaden (PPZ), but they were still sensitive to the ALS inhibitors mesosulfuron-methyl and pyroxsulam. An Ile-2041-Asn mutation was identified in both resistant individual plants. The copy number and relative expression of the ACCase gene in the resistant population were not significantly different from those in the S1496 population. Under the application of 2160 g ai ha -1 of clodinafop-propargyl, the fresh weight of the R1623 population was reduced to 74.9%; however, pretreatment with the application of the cytochrome P450 inhibitor malathion and the GST inhibitor NBD-Cl reduced the fresh weight to 50.91% and 47.16%, respectively, which proved the presence of metabolic resistance. This is the first report of an Ile-2041-Asn mutation and probable metabolic resistance in A. fatua, resulting in resistance to clodinafop-propargyl.

Enhanced metabolic resistance mechanism endows resistance to metamifop in Echinochloa crus-galli (L.) P. Beauv

Barnyardgrass (Echinochloa crus-galli (L.) P. Beauv.), one of the worst weeds in paddy fields in China, has been frequently reported evolving resistance to acetyl-CoA carboxylase (ACCase) inhibiting herbicides. However, in the previous research, more attention was paid to target-site resistance (TSR) mechanisms, the non-target-site resistance (NTSR) mechanisms have not been well-established. In this study, the potential mechanism of resistance in a metamifop-resistant E. crus-galli collected from Kunshan city, Jiangsu Province, China was investigated. Dose-response assays showed that the phenotypic resistant population (JS-R) has evolved 4.3-fold resistance to metamifop compared with the phenotypic susceptible population (YN-S). The ACCase CT gene sequencing and relative ACCase gene expression levels studies showed that no mutations were detected in the ACCase CT gene in both YN-S and JS-R, and there was no significant difference in the relative ACCase gene expression between YN-S and JS-R. After the pre-processing of glutathione-S-transferase (GSTs) inhibitor NBD-Cl, the resistance level of JS-R to metamifop was reversed 18.73%. Furthermore, the GSTs activity of JS-R plants was significantly enhanced compared to that of YN-S plants. UPLC-MS/MS revealed that JS-R plants had faster metabolic rates to metamifop than YN-S plants. Meanwhile, the JS-R popultion exhibited resistant to cyhalofop-butyl and penoxsulam. In summary, this study presented a novel discovery regarding the global emergence of metabolic resistance to metamifop in E. crus-galli. The low-level resistance observed in the JS-R population was not found to be related to TSR but rather appeared to be primarily associated with the overexpression of genes in the GSTs metabolic enzyme superfamily.

Investigating the effects of mesotrione/atrazine-based herbicide on honey bee foragers

A mixture of the herbicides mesotrione and atrazine (Calaris®) is a widely used herbicide in agriculture in several countries. However, the possible toxicological effects of this formulation on non-target organisms require investigation. In this study, the effects of acute oral exposure to Calaris® were evaluated in Apis mellifera foragers. The effect of seven different concentrations of Calaris® on survival and sucrose consumption was studied, while the recommended concentration for field use (FC) and its 10× dilution (0.1 FC) were used to assess overall locomotor activity, respiratory rate, flight, midgut morphology, oxidative and nitrosative stresses, and hemocyte counting. The exposure to FC or 0.1 FC decreased locomotor activity and induced damage to the midgut epithelium. Additionally, the two tested concentrations reduced superoxide dismutase activity, nitric oxide levels, and total hemocyte count. FC also increased malondialdehyde content and 0.1 FC increased respiratory rate and decreased the proportion of prohemocytes. Overall, our findings evidenced significant harmful effects on A. mellifera foragers resulting from the ingestion of the Calaris® herbicide.

Comprehensive insights into herbicide resistance mechanisms in weeds: a synergistic integration of transcriptomic and metabolomic analyses

Omics techniques, including genomics, transcriptomics, proteomics, and metabolomics have smoothed the researcher's ability to generate hypotheses and discover various agronomically relevant functions and mechanisms, as well as their implications and associations. With a significant increase in the number of cases with resistance to multiple herbicide modes of action, studies on herbicide resistance are currently one of the predominant areas of research within the field of weed science. High-throughput technologies have already started revolutionizing the current molecular weed biology studies. The evolution of herbicide resistance in weeds (particularly via non-target site resistance mechanism) is a perfect example of a complex, multi-pathway integration-induced response. To date, functional genomics, including transcriptomic and metabolomic studies have been used separately in herbicide resistance research, however there is a substantial lack of integrated approach. Hence, despite the ability of omics technologies to provide significant insights into the molecular functioning of weeds, using a single omics can sometimes be misleading. This mini-review will aim to discuss the current progress of transcriptome-based and metabolome-based approaches in herbicide resistance research, along with their systematic integration.

Enhanced metabolic ability enabled wild panicgrass (Panicum miliaceum L. var. ruderale kit.) resistance to ALS inhibitor herbicide

Wild panicgrass (Panicum miliaceum L. var. ruderale kit.) is an annual grass weed that primarily occurs in maize fields. Nicosulfuron is a widely used selective herbicide that effectively controls gramineous weeds in maize fields. However, owing to its long-term and extensive application, the control of P. miliaceum has been substantially reduced. The objective of this study was to determine the resistance pattern to ALS inhibitors in P. miliaceum and investigate the underlying resistance mechanisms. These are important for guiding the prevention and eradication of resistant weeds. Whole plant bioassays showed P. miliaceum had evolved high levels of resistance to nicosulfuron and multiple resistance to atrazine and mesotrione. The ALS gene sequence results indicated the absence of mutations in the resistant population. Additionally, there was no significant difference found in the inhibition rate of the ALS enzyme activity (I50) between the resistant and sensitive populations. Following the application of malathion the resistant P. miliaceum population became more sensitive to nicosulfuron. At 96 h after application of nicosulfuron, glutathione-S-transferase activity in the resistant population was significantly higher than that in the susceptible population. The study reveals that the main cause of resistance to ALS inhibitor herbicide in P. miliaceum is likely increased metabolism of herbicides. These findings may assist in devising effective strategies for preventing and eliminating resistant P. miliaceum.

Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense

Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.

Isolation and purification of potential weed inhibitors from Mimosa pigra L

The diversity in structure and herbicidal properties detected in natural phytotoxic compounds could bring about advantages for development bio-herbicides. The present study was carried out search for potential weed inhibitors from the parts of Mimosa pigra L. The ethyl acetate (EtOAc) extract of leaf of M. pigra showed inhibitory activity during the time that Echinochloa crus-galli (barnyardgrass) germinates and grows, which is greater than that of other extracts. From this active extract, potent growth inhibitors were isolated and identified by column chromatography (CC), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (¹H and ¹³C NMR). The six compounds were purified in this study namely: lupeol (C1, 13.2 mg), stigmastane-3,6-dione (C2, 14.7 mg), quercetin (C3, 20.2 mg), chrysoeriol (C4, 28 mg), methyl gallate (C5, 21.5 mg) and daucosterol (C6, 16.0 mg). The C2 (quercetin) compound completely inhibited the emergency, shoot height and root length of E. crus-galli at 1 mg/mL concentration (IC₅₀ shoot height = 0.56 mg/mL). This was also the first study to report the isolation and allelopathic activity of lupeol, chrysoeriol and daucosterol from M. pigra leaf. Findings of this study highlighted that quercetin from M. pigra may become bio-herbicide to control barnyard grass and other grass weeds for the development of safe agriculture.

Comparative proteomic and physiological analyses reveal tribenuron-methyl phytotoxicity and nontarget-site resistance mechanisms in Brassica napus

The application of herbicides is the most effective strategy for weed control and the development of herbicide-resistant crops will facilitate the weed management. The acetolactate synthase-inhibiting herbicide, tribenuron-methyl (TBM), is broadly used for weed control. However, its application in rapeseed field is restricted since rapeseed is sensitive to TBM. Herein, an integrated study of cytological, physiological and proteomic analysis of the TBM-resistant rapeseed mutant M342 and its wild-type (WT) plants was conducted. After TBM spraying, M342 showed improved tolerance to TBM, and proteins implicated in non-target-site resistance (NTSR) to herbicides had a significantly higher level in M342 as compared with the WT. Differentially accumulated proteins (DAPs) between these two genotypes were enriched in glutathione metabolism and oxidoreduction coenzyme metabolic process, which protected the mutant from oxidative stress triggered by TBM. Important DAPs related to stress or defence response were up-accumulated in M342 regardless of the TBM treatment, which might serve as the constitutive part of NTSR to TBM. These results provide new clues for further exploration of the NTSR mechanism in plants and establish a theoretical basis for the development of herbicide-resistant crops.

The social foundations for re-solving herbicide resistance in Canterbury, New Zealand

Synthetic herbicides have revolutionised agricultural weed control. Herbicide resistance (HR) is a natural process through which weeds evolve to be no longer susceptible to a herbicide. Repeated use of similar herbicides can lead to the proliferation of resistant weed populations, with detrimental on-farm effects. To date, 267 weed species worldwide are resistant to at least one herbicide. Yet, achieving universal uptake of best practice principles to manage HR remains difficult. Historically not a high priority for New Zealand cropping farmers, resistance may be more prevalent than commonly assumed. This article contributes to emerging national management strategies and the international scholarship on the human dimensions of HR. Regarding resistance as a socio-biological challenge, we draw on qualitative social research with agricultural stakeholders in New Zealand's main cropping region to outline important psychosocial preconditions for effective resistance management. Our findings show that these preconditions include: influencing awareness and attitudes, knowledge and skills; approaching HR as a shared responsibility; and supporting long-term and holistic thinking. We conclude that these preconditions form the social foundations for agricultural stakeholders' capacity to enact best practice principles to continuously re-solve HR. This novel framing allows analytical differentiation between the capacity and ability to act, with practical recommendations and future research needing to address both components of effective HR management.

First report on ALS herbicide resistance in barnyardgrass (Echinochloa crus-galli) from rice fields of India

Bispyribac-sodium, a herbicide that inhibits acetolactate synthase (ALS), is frequently used in rice fields in India to control weeds, including the most common noxious weed, barnyardgrass. However, rice growers have recently reported reduced control of barnyardgrass with bispyribac-sodium. Hence, a large-scale survey was carried out to assess bispyribac-sodium resistance in Chhattisgarh and Kerala, two rice-growing states. Open-field pot experiments were conducted for 2 yr to confirm resistance to bispyribac-sodium. Of the 37 biotypes tested, 30% (11) survived the recommended label rate of bispyribac-sodium (25 g ai ha−1). The effective rate of bispyribac-sodium required to achieve 50% control (ED50) of putative resistant biotypes ranged from 18 to 41 g ha−1, whereas it was about 10 g ha−1 for susceptible biotypes. This suggests that putative biotypes were two to four times more resistant to bispyribac-sodium. At 6 d after herbicide application, an in vitro enzyme assay demonstrated higher ALS enzyme activity in putative resistant biotypes (66% to 75%) compared with susceptible biotypes (48% to 52%). This indicates the presence of an insensitive ALS enzyme in those biotypes and a target site mutation as a possible mechanism for resistance. Whole-plant bioassays also suggested that the resistance problem is more widespread in Chhattisgarh than in Kerala. This study confirmed the first case of evolved resistance in barnyardgrass to bispyribac-sodium in rice fields of India.

Persistence of Abscisic Acid Analogs in Plants: Chemical Control of Plant Growth and Physiology

Abscisic acid (ABA) is a plant hormone that regulates numerous plant processes, including plant growth, development, and stress physiology. ABA plays an important role in enhancing plant stress tolerance. This involves the ABA-mediated control of gene expression to increase antioxidant activities for scavenging reactive oxygen species (ROS). ABA is a fragile molecule that is rapidly isomerized by ultraviolet (UV) light and catabolized in plants. This makes it challenging to apply as a plant growth substance. ABA analogs are synthetic derivatives of ABA that alter ABA's functions to modulate plant growth and stress physiology. Modifying functional group(s) in ABA analogs alters the potency, selectivity to receptors, and mode of action (i.e., either agonists or antagonists). Despite current advances in developing ABA analogs with high affinity to ABA receptors, it remains under investigation for its persistence in plants. The persistence of ABA analogs depends on their tolerance to catabolic and xenobiotic enzymes and light. Accumulated studies have demonstrated that the persistence of ABA analogs impacts the potency of its effect in plants. Thus, evaluating the persistence of these chemicals is a possible scheme for a better prediction of their functionality and potency in plants. Moreover, optimizing chemical administration protocols and biochemical characterization is also critical in validating the function of chemicals. Lastly, the development of chemical and genetic controls is required to acquire the stress tolerance of plants for multiple different uses.

Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.

Enhanced Herbicide Metabolism and Target-Site Mutations Confer Multiple Resistance to Fomesafen and Nicosulfuron in Amaranthus retroflexus L

Amaranthus retroflexus L. is a highly competitive broadleaf weed of corn-soybean rotation in northeastern China. In recent years, the herbicide(s) resistance evolution has been threatening its effective management in crop fields. One resistant A. retroflexus (HW-01) population that survived the protoporphyrinogen oxidase (PPO) inhibitor fomesafen and acetolactate synthase (ALS) inhibitor nicosulfuron applied at their field-recommended rate was collected from a soybean field in Wudalianchi City, Heilongjiang Province. This study aimed to investigate the resistance mechanisms of fomesafen and nicosulfuron and determine the resistance profile of HW-01 to other herbicides. Whole plant dose-response bioassays revealed that HW-01 had evolved resistance to fomesafen (50.7-fold) and nicosulfuron (5.2-fold). Gene sequencing showed that the HW-01 population has a mutation in PPX2 (Arg-128-Gly) and a rare mutation in ALS (Ala-205-Val, eight/twenty mutations/total plants). In vitro enzyme activity assays showed that ALS extracted from the HW-01 plants was less sensitive to nicosulfuron (3.2-fold) than ST-1 plants. Pre-treatment with the cytochrome P450 inhibitors malathion, piperonyl butoxide (PBO), 3-amino-1,2,4-triazole (amitrole), and the GSTs inhibitor 4-chloro-7-nitrobenzofurazan (NBD-Cl) significantly increased fomesafen and nicosulfuron sensitivity in the HW-01 population compared with that of the sensitive (S) population ST-1. Moreover, the rapid fomesafen and nicosulfuron metabolism in the HW-01 plants was also confirmed via HPLC-MS/MS analysis. Furthermore, the HW-01 population showed multiple resistance (MR) to PPO, ALS, and PSII inhibitors, with resistance index (RI) values ranging from 3.8 to 9.6. This study confirmed MR to PPO-, ALS-, and PSII-inhibiting herbicides in the A. retroflexus population HW-01, as well as confirming that the cytochrome P450- and GST-based herbicide metabolic along with TSR mechanisms contribute to their multiple resistance to fomesafen and nicosulfuron.

Inheritance of 2,4-dichlorophenoxyacetic acid (2,4-D) resistance in Amaranthus palmeri

In this study, the inheritance of 2,4-D resistance in a multiple herbicide-resistant Palmer amaranth (KCTR) was investigated. Direct and reciprocal crosses were performed using 2,4-D-resistant KCTR and susceptible KSS plants to generate F₁ progenies. 2,4-D dose-response assays were conducted to evaluate the response of progenies from each F₁ family along with KCTR and KSS plants in controlled environmental growth chambers. Additionally, 2,4-D-resistant male and female plants from each of the F₁ families were used in pairwise crosses to generate pseudo-F₂ families. Segregation (resistance or susceptibility) of progenies from the F₂ families in response to a discriminatory rate of 2,4-D (i.e., 560 g ae ha^-1) was evaluated. Dose-response analysis of F₁ progenies derived from direct and reciprocal crosses suggested that the 2,4-D resistance in KCTR is a nuclear trait. Chi-square analyses of F₂ segregation data implied that 2,4-D resistance in KCTR is controlled by multiple gene(s). Overall, our data suggest that the 2,4-D resistance in KCTR Palmer amaranth is a nuclear inherited trait controlled by multiple genes. Such resistance can spread both via pollen or seed-mediated gene flow. In future, efforts will be directed towards identifying genes mediating 2,4-D resistance in KCTR population.

Involvement of miRNAs in Metabolic Herbicide Resistance to Bispyribac-Sodium in Echinochloa crus-galli (L.) P. Beauv

Several mechanisms involved in weed herbicide resistance are unknown, particularly those acting at the epigenetic level, such as the capacity of small-non-coding RNAs (sncRNAs) to target messenger RNAs of genes involved in herbicide detoxification. The transcription of these sncRNAs is stimulated by epigenetic factors, thereby affecting gene expression. This study was carried out in order to evaluate, for the first time in Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass), the capacity of miRNAs to regulate the expression of genes associated with bispyribac-sodium detoxification. The expression profiles of eight miRNAs with a high degree of complementarity (≥80%) with mRNAs of genes involved in herbicide detoxification (CYP450, GST and eIF4B) were determined by qRT-PCR before and after herbicide spraying. Five of the miRNAs studied (gra-miR7487c, gma-miR396f, gra-miR8759, osa-miR395f, ath-miR847) showed an increased expression after herbicide application in both susceptible and resistant biotypes. All the miRNAs, except gra-miR8759, were more highly expressed in the herbicide-resistant biotypes. In specimens with increased expression of miRNAs, we observed reduced expression of the target genes. The remaining three miRNAs (ata-miR166c-5p, ath-miR396b-5p and osa-miR5538) showed no over-expression after herbicide treatment, and no difference in expression was recorded between susceptible and resistant biotypes. Our results represent a first overview of the capacity of miRNAs to regulate the expression of genes involved in bispyribac-sodium detoxification in the genus Echinochloa. Further research is required to identify novel miRNAs and target genes to develop more focused and sustainable strategies of weed control.

Survey of ACCase and ALS resistance in winter annual grasses identifies target-site and nontarget-site imazamox resistance in Secale cereale

BACKGROUND

Early detection of herbicide resistance in weeds is crucial for successful implementation of integrated weed management. We conducted a herbicide resistance survey of the winter annual grasses feral rye (Secale cereale), downy brome (Bromus tectorum), and jointed goatgrass (Aegilops cylindrica) from Colorado winter wheat production areas for resistance to imazamox and quizalofop.

RESULTS

All samples were susceptible to quizalofop. All downy brome and jointed goatgrass samples were susceptible to imazamox. Out of 314 field collected samples, we identified three feral rye populations (named A, B, and C) that were imazamox resistant. Populations B and C had a target-site mechanism with mutations in the Ser653 residue of the acetolactate synthase (ALS) gene to Asn in B and to Thr in C. Both populations B and C had greatly reduced ALS in vitro enzyme inhibition by imazamox. ALS feral rye protein modeling showed that steric interactions induced by the amino acid substitutions at Ser653 impaired imazamox binding. Individuals from population A had no mutations in the ALS gene. The ALS enzyme from population A was equally sensitive to imazamox as to known susceptible feral rye populations. Imazamox was degraded two times faster in population A compared with a susceptible control. An oxidized imazamox metabolite formed faster in population A and this detoxification reaction was inhibited by malathion.

CONCLUSION

Population A has a nontarget-site mechanism of enhanced imazamox metabolism that may be conferred by cytochrome P450 enzymes. This is the first report of both target-site and metabolism-based imazamox resistance in feral rye. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

An Asp376Glu substitution in ALS gene and enhanced metabolism confers high tribenuron-methyl resistance in Sinapis alba

Acetolactate synthase (ALS) inhibiting herbicides (group 2) have been widely applied for the last 20 years to control Sinapis alba in cereal crops from southern Spain. In 2008, a tribenuron-methyl (TM) resistant (R) S. alba population was first reported in a cereal field in Malaga (southern Spain). In 2018, three suspected R S. alba populations (R1, R2 and R3) to TM were collected from three different fields in Granada (southern Spain, 100 km away from Malaga). The present work aims to confirm the putative resistance of these populations to TM and explore their resistance mechanisms. Dose-response assays showed that the R1, R2 and R3 populations ranging between 57.4, 44.4 and 57.1 times more resistance to TM than the susceptible population (S). A mutation in the ALS gene (Asp376Glu) was detected in the Rs S. alba populations. ¹⁴C-metabolism studies show that metabolites and TM were changing significantly faster in the R than in the S plants. Alternative chemical control trials showed that 2,4-D and MCPA (auxin mimics), glyphosate (enolpyruvyl shikimate phosphate synthase,EPSPS, inhibitor-group 9), metribuzin (PSII inhibitors/Serine 264 Binders, -group 5) and mesotrione (hydroxyphenyl pyruvate dioxygenase, HPPD, inhibitor-group 27) presented a high control of the four populations of S. alba tested, both S and R. Based on these results, it is the first case described where the Asp376Glu mutation and P450-mediated metabolism participates in resistance to TM in S. alba. Comparing these results with those found in the S. alba population in Malaga in 2008, where the resistance was TSR type (Pro197Ser), we can suggest that despite the geographical proximity (over 100 km), the resistance in these cases was due to different evolutionary events.

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

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

Dinitroaniline herbicides: a comprehensive review of toxicity and side effects on animal non-target organisms

The widespread use of herbicides has increased concern about the hazards and risks to animals living in terrestrial and aquatic ecosystems. A comprehensive understanding of their effective action at different levels of biological organization is critical for establishing guidelines to protect ecosystems and human health. Dinitroanilines are broad-spectrum pre-emergence herbicides currently used for weed control in the conventional agriculture. They are considered extremely safe agrochemicals because they act specifically on tubulin proteins and inhibit shoot and root growth of plants. However, there is a lack of toxicity information regarding the potential risk of exposure to non-target organisms. The aim of the present review is to focus on side effects of the most commonly used active ingredients, e.g. pendimethalin, oryzalin, trifluralin and benfluralin, on animal non-target cells of invertebrates and vertebrates. Acute toxicity varies from slightly to high in terrestrial and aquatic species (i.e. nematodes, earthworms, snails, insects, crustaceans, fish and mammals) depending on the species-specific ability of tested organisms to adsorb and discharge toxicants. Cytotoxicity, genotoxicity and activation of oxidative stress pathways as well as alterations of physiological, metabolic, morphological, developmental and behavioural traits, reviewed here, indicate that exposure to sublethal concentrations of active ingredients poses a clear hazard to animals and humans. Further research is required to evaluate the molecular mechanisms of action of these herbicides in the animal cell and on biological functions at multiple levels, from organisms to communities, including the effects of commercial formulations.

Multiple resistance to ALS-inhibiting and PPO-inhibiting herbicides in Chenopodium album L. from China

Common lambsquarters (Chenopodium album L.) is a broadleaf weed that can severely damage soybean fields. Two C. album populations (1744 and 1731) suspected resistant to imazethapyr were investigated for resistance levels to imazethapyr, thifensulfuron-methyl, and fomesafen and their resistance mechanisms were investigated. Whole-plant dose-response assays revealed that, compared to the susceptible (S) population, the 1744 population was 16.5-fold resistant to imazethapyr, slightly resistant to thifensulfuron-methyl (resistance index [R/S], <3). The 1731 population was 18.8-fold resistant to imazethapyr, 2.9-fold resistant to thifensulfuron-methyl, and 5.1-fold resistant to fomesafen. In vitro acetolactate synthase (ALS) assays showed 17.1-fold and 19.3-fold resistance levels of 1744 and 1731 populations to imazethapyr respectively. ALS gene sequence analysis identified Ala122Thr amino acid substitution in the 1744 population and Ser653Thr amino acid substitution in the 1731 population. No mutations of the protoporphyrinogen oxidase (PPO) gene were detected. However, pre-treatment with malathion reversed fomesafen resistance, suggesting nontarget-site resistance mechanisms likely play a role in the 1731 population.

Investigating resistance levels to cyhalofop-butyl and mechanisms involved in Chinese sprangletop (Leptochloa chinensis L.) from Anhui Province, China

Chinese sprangletop (Leptochloa chinensis (L.) Nees) is a common grass species that severely threatens rice (Oryza sativa L.) cropping systems globally. Cyhalofop-butyl is a highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide widely used for control of this species in China. However, some L. chinensis populations have gradually evolved resistance to this herbicide in recent years. To better understand the cyhalofop-butyl resistance status of L. chinensis in the major rice planting area of the middle-lower Yangtze River basin, 73 populations collected from the rice fields across Anhui Province were investigated for cyhalofop-butyl susceptibility and potential herbicide resistance-conferring mutations. Single-dose testing indicated that of the 73 populations, 25 had evolved resistance to cyhalofop-butyl and were separately classified as "RRR" and "RR" populations according to their fresh weight reductions, 8 had a high risk of evolving cyhalofop-butyl resistance and were classified as "R?" populations, and 40 were susceptible and classified as "S" populations. Whole-plant dose-response experiments showed that the resistance index (RI) of these R?, RR, and RRR populations to cyhalofop-butyl ranged from 2.47 to 36.94. Target gene sequencing identified seven ACCase resistance mutations (I1781L, W1999C, W2027S, W2027L, W2027C, I2041N, and D2078G), with W1999C and W2027C the two most common detected in about three quarters of all the resistant populations. Seven populations including LASC3, BBHY1, AQQS1, HFFD3, HFFD4, AQWJ1, and HFLJ6 each carrying a specific ACCase mutation were tested for their cross- and multiple-resistance patterns. Compared with a standard susceptible population HFLY1, the seven resistant populations showed distinct cross-resistance. All had low- to high-level cross-resistance to metamifop (RIs ranging from 6.16 to 17.65), fenoxaprop-P-ethyl (RIs ranging from 6.39 to 24.08), and quizalofop-P-ethyl (RIs ranging from 2.20 to 10.25), but responded differently to clodinafop-propargyl and clethodim. Multiple-resistance testing suggested that the seven resistant populations were all susceptible to the 4-hydroxyphenylpyruvate dioxygenase inhibitor tripyrasulfone, the protoporphyrinogen oxidase inhibitor oxyfluorfen, and the auxin mimic herbicide florpyrauxifen. In conclusion, this study has shown that cyhalofop-butyl resistance was prevalent in L. chinensis in Anhui Province, China, and target site mutation was one of the most common resistance mechanisms.

Comparison between the mechanisms of Clearfield ® wheat and Lolium rigidum multiple resistant to acetyl CoA carboxylase and acetolactate synthase inhibitors

Clearfield® wheat (Triticum aestivum) have helped eliminate the toughest grasses and broadleaf weeds in Spain since 2005. This crop production system includes other tolerant cultivars to the application of imidazolinone (IMI) herbicides. However, the continuous use and off-label rates of IMI herbicides can contribute to the development of resistance in Lolium rigidum and other weed species. In this research, the main objectives were to study the resistance mechanisms to acetolactate synthase (ALS) and acetyl coenzyme A carboxylase (ACCase) inhibitors in a L. rigidum accession (LrR) from a Clearfield® wheat field, with a long history rotating these IMI-tolerant crops and compare them with those present in the IMI-tolerant wheat. The resistance to ACCase inhibitors in LrR was due to point mutations (Ile1781Leu plus Asp2078Gly) of the target site gene plus an enhanced herbicide metabolism (EHM), on the other hand, in wheat accessions was due only by EHM. Mechanisms involved in the resistance to ALS inhibitors were both point mutations of the target gene and EHM in the IMI-tolerant wheat, while only evidence of mutation (Trp574Leu) was found in the multiple herbicide resistant L. rigidum accession. This research demonstrates that if crop rotation is not accompanied by the use of alternative sites of action in herbicide-tolerant crops, resistant weeds to herbicide to which crops are tolerant, can easily be selected. Moreover, repeated and inappropriate use of Clearfield® crops and herbicide rotations can lead to the evolution of multiple resistant weeds, as shown in this study, and have also inestimable environmental impacts.

Primary metabolism in an Amaranthus palmeri population with multiple resistance to glyphosate and pyrithiobac herbicides

The objective of this work was to characterize the resistance mechanisms and the primary metabolism of a multiple resistant (MR) population of Amaranthus palmeri to glyphosate and to the acetolactate synthase (ALS) inhibitor pyrithiobac. All MR plants analysed were glyphosate-resistant due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. Resistance to pyrithiobac was more variable among individuals and was related to point mutations at five positions in the ALS gene sequence: A122, A205, W574, S653 and G654. All MR plants were heterozygous for W574, the most abundant mutation. In nontreated plants, the presence of mutations did not affect ALS functionality, and plants with the W574L mutation showed the highest ALS resistance level to pyrithiobac. The accumulation of the transcripts corresponding to several genes of the aromatic amino acid (AAA) and branched-chain amino acid (BCAA) pathways detected in nontreated MR plants indicated additional effects of EPSPS gene amplification and ALS mutations. The physiological performance of the MR population after treatment with glyphosate and/or pyrithiobac was compared with that of a sensitive (S) population. The increase induced in total soluble sugars, AAA or BCAA content by both herbicides was higher in the S population than in the MR population. Physiological effects were not exacerbated after the mixture of both herbicides in S or in MR populations. This study provides new insights into the physiology of a multiple resistant A. palmeri, which could be very useful for achieving effective management of this weed.

Expression Pattern of Entire Cytochrome P450 Genes and Response of Defenses in a Metabolic-Herbicide-Resistant Biotype of Polypogon fugax

Enhanced herbicide metabolism mediated by cytochrome P450s has been proposed as one of the major mechanisms of resistance to fenoxaprop-P-ethyl in a metabolic-herbicide-resistant biotype of Asia minor bluegrass (Polypogon fugax Nees ex Steud.). Upon pre-treatment with the P450 inhibitor piperonyl butoxide, a remarkable reduction in metabolic rates of the phytotoxic fenoxaprop-P has been observed in the resistant plants, implying that constitutive and/or fenoxaprop-P-ethyl-induced up-regulation of specific P450 isoforms are involved in the fenoxaprop-P-ethyl resistance. However, which P450 gene(s) were responsible for the metabolic resistance is still unknown. In this present study, based on the abundant gene resources of P. fugax established previously, a total of 48 putative P450 genes were isolated from the metabolic-herbicide-resistant plants and used for gene expression analysis. The most suitable reference genes for accurate normalization of real-time quantitative PCR data were first identified in P. fugax and recognized as actin (ACT), 18S rRNA (18S), and ribulose-1,5-bisphosphate carboxylase oxygenase (RUBP) under fenoxaprop-P-ethyl stress, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and elongation factor 1α (EF1α) under mesosulfuron-methyl stress, and ACT, EF1α, eukaryotic initiation factor 4a (EIF4A), and 25S rRNA (25S) at different growth stages. Expression analysis of the putative P450 genes revealed that six genes, respectively, annotated as CYP709B1, CYP71A1-4, CYP711A1, CYP78A9, P450-11, and P450-39 were up-regulated more than 10-fold in the resistant plants by fenoxaprop-P-ethyl treatment, and all of them exhibited constitutively and/or herbicide-induced higher transcript levels in the fenoxaprop-P-ethyl-resistant than in the susceptible plants. Three genes, respectively, annotated as CYPRO4, CYP313A4, and CYP51H11 constantly up-regulated in the resistant than in the susceptible plants after fenoxaprop-P-ethyl treatment. Up-regulated expressions of these specific P450 genes were consistent with the higher P450 contents determined in the resistant plants. These results will help to elucidate the mechanisms for P450-mediated metabolic-herbicide resistance in P. fugax as well as other grass weed species.

Identification of essential genes involved in metabolism-based resistance mechanism to fenoxaprop-P-ethyl in Polypogon fugax

BACKGROUND

Metabolic resistance is a worldwide concern for weed control but has not yet been well-characterized at the genetic level. Previously, we have identified an Asia minor bluegrass (Polypogon fugax Nees ex Steud.) population AHHY exhibiting cytochrome P450 (P450)-involved metabolic resistance to fenoxaprop-P-ethyl. In this study, we aimed to confirm the metabolic fenoxaprop-P-ethyl resistance in AHHY and uncover the potential herbicide metabolism-related genes in this economically damaging weed species.

RESULTS

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays indicated the metabolic rates of fenoxaprop-P-ethyl were significantly faster in resistant (R, AHHY) than in susceptible (S, SDTS) plants. The amount of phytotoxic fenoxaprop-P peaked at 12 h after herbicide treatment (HAT) and started to decrease at 24 HAT in both biotypes. R and S plants at 24 HAT were sampled to conduct isoform-sequencing (Iso-Seq) and RNA-sequencing (RNA-Seq). A reference transcriptome containing 24 972 full-length isoforms was obtained, of which 24 329 unigenes were successfully annotated. Transcriptomic profiling identified 28 detoxifying enzyme genes constitutively and/or herbicide-induced up-regulated in R than in S plants. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed 17 genes were consistently up-regulated in R and its F1 generation plants. They were selected as potential fenoxaprop-P-ethyl metabolism-related genes, including ten P450s, one glutathione-S-transferase, one UDP-glucosyltransferase, and five adenosine triphosphate (ATP)-binding cassette transporters.

CONCLUSION

This study revealed that the enhanced rates of fenoxaprop-P-ethyl metabolism in P. fugax were very likely driven by the herbicide metabolism-related genes. The transcriptome data generated by Iso-Seq combined with RNA-Seq will provide abundant gene resources for understanding the molecular mechanisms of resistance in P. fugax.

Hierarchical cluster analysis of herbicide modes of action reveals distinct classes of multiple resistance in weeds

BACKGROUND

The number of weed species resistant to multiple herbicide modes of action (MoAs) has increased over the last 30 years and may in the future render existing herbicide MoAs obsolete for many cropping systems. Yet few predictive tools exist to manage this risk. Using a worldwide dataset of weed species resistant to multiple herbicide MoAs, hierarchical clustering was used to classify MoAs into similar groups in relation to the suite of resistant weed species they have in common. Network analyses then were used to explore the relative importance of species prevalence and similarity in cluster patterns.

RESULTS

Hierarchical clustering identified three similarly sized clusters of herbicide MoAs that were linked by the co-occurrence of resistant weeds: Herbicide Resistance Action Committee (HRAC) groups 2, 4, 5 and 9; HRAC groups 12, 14 and 15; and HRAC groups 1, 3 and 22. Cluster membership was consistent with similarities in the physiological or biochemical target of the herbicide MoAs. Network analyses revealed that the number of weed species resistant to two different MoAs was related to the number of weeds known to be resistant to each individual herbicide MoA.

CONCLUSIONS

Hierarchical cluster analysis provided new insights into the risk of weeds becoming resistant to more than one herbicide MoA. By clustering herbicide MoAs into three distinct groups, the potential exists for farmers to manage resistance by rotating herbicides between rather than within clusters, as far as crop, weed and environmental conditions allow.

Multiple herbicide resistance in Eleusine indica from sugarcane fields in China

Long-term reliance on herbicide weed control has led to resistance evolution in Eleusine indica in sugarcane fields of Guangxi Zhuang autonomous region. Ninety-six E. indica lines were collected from this region, and their response was tested to six herbicides: glyphosate; glufosinate; PSII-inhibitors diuron and atrazine; and PSI inhibitors paraquat and diquat. Target-site resistance mechanisms were examined in specific lines with multiple resistance to three herbicide modes of action. Of 96 E. indica lines, 51, 26, and 24 lines had resistance to diuron, atrazine, and diquat, respectively, while 14 and 9 had resistance to paraquat and glyphosate. Among 25 lines tested with multiple resistance, 7 lines exhibited resistance to three herbicide modes of action. In two multiple resistant lines (GXER2, GXER5), amplification/over-expression/mutations of the EPSPS gene contributed to the very high-level (up to 109-fold) glyphosate resistance. No target-site mutations/over-expression were identified in the psbA gene in these two lines, so non-target-site resistance mechanisms were likely responsible for the low-level (3-fold) resistance to the PSII herbicides diuron and atrazine. A high-level (23-fold) of paraquat resistance was observed in GXER5, and a low-level (5-fold) paraquat resistance was found in GXER2. Multiple herbicide resistance in E. indica has evolved in sugarcane fields of Guangxi Zhuang autonomous region with diverse resistance mechanisms. Therefore, diversified weed control tactics should be adopted to prevent this weed.

Drought exposure leads to rapid acquisition and inheritance of herbicide resistance in the weed Alopecurus myosuroides

Globally, herbicide resistance in weeds poses a threat to food security. Resistance evolves rapidly through the co‐option of a suite of physiological mechanisms that evolved to allow plants to survive environmental stress. Consequently, we hypothesize that stress tolerance and herbicide resistance are functionally linked. We address two questions: (i) does exposure to stress in a parental generation promote the evolution of resistance in the offspring? (ii) Is such evolution mediated through non‐genetic mechanisms? We exposed individuals of a grass weed to drought, and tested whether this resulted in herbicide resistance in the first generation. In terms of both survival and dry mass, we find enhanced resistance to herbicide in the offspring of parents that had been exposed to drought. Our results suggest that exposure of weeds to drought can confer herbicide resistance in subsequent generations, and that the mechanism conferring heritability of herbicide resistance is non‐genetic.

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.

Biotechnological Road Map for Innovative Weed Management

In most agriculture farmlands, weed management is predominantly reliant on integrated weed management (IWM) strategies, such as herbicide application. However, the overuse and misuse of herbicides, coupled with the lack of novel active ingredients, has resulted in the uptrend of herbicide-resistant weeds globally. Moreover, weedy traits that contribute to weed seed bank persistence further exacerbate the challenges in weed management. Despite ongoing efforts in identifying and improving current weed management processes, the pressing need for novel control techniques in agricultural weed management should not be overlooked. The advent of CRISPR/Cas9 gene-editing systems, coupled with the recent advances in "omics" and cheaper sequencing technologies, has brought into focus the potential of managing weeds in farmlands through direct genetic control approaches, but could be achieved stably or transiently. These approaches encompass a range of technologies that could potentially manipulate expression of key genes in weeds to reduce its fitness and competitiveness, or, by altering the crop to improve its competitiveness or herbicide tolerance. The push for reducing or circumventing the use of chemicals in farmlands has provided an added incentive to develop practical and feasible molecular approaches for weed management, although there are significant technical, practical, and regulatory challenges for utilizing these prospective molecular technologies in weed management.

Non-target-site resistance mechanism of barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] to florpyrauxifen-benzyl

BACKGROUND

Florpyrauxifen-benzyl (FPB) is an arylpicolinate herbicide (Group IV) for barnyardgrass control in rice. One susceptible (Sus) and three putative FPB-resistant (R1, R2, and R3) barnyardgrass biotypes were selected based on resistant/susceptible (R/S) ratios obtained from dose-response tests and used to investigate the potential resistance mechanisms.

RESULTS

Based on visual control results, the R/S ratios of barnyardgrass biotypes R1, R2, and R3 were 60-, 33-, and 16-fold greater than the Sus standard, respectively. Sequencing results of TIR1 and AFB genes in the tested barnyardgrass revealed no difference between Sus and R barnyardgrass biotypes. Absorption of [¹⁴ C]-FPB in Sus barnyardgrass increased over time and reached 90%, which was >10 percentage points greater than that in R biotypes. The [¹⁴ C]-FPB absorption in all R barnyardgrass equilibrated after 48 h. For both Sus and R barnyardgrass, most [¹⁴ C]-FPB absorbed was present in the treated leaf (79.8-88.8%), followed by untreated aboveground (9.5-18.6%) and belowground tissues (1.3-2.2%). No differences in translocation were observed. Differences between Sus and R barnyardgrass biotypes were found for FPB metabolism. Production of the active metabolite, florpyrauxifen-acid, was greater in Sus barnyardgrass (21.5-52.1%) than in R barnyardgrass (5.5-34.9%).

CONCLUSION

In conclusion, reductions in FPB absorption and florpyrauxifen-acid production may contribute to the inability to control barnyardgrass with FPB. © 2021 Society of Chemical Industry.

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.

Vegetative and Fecundity Fitness Benefit Found in a Glyphosate-Resistant Eleusine indica Population Caused by 5-Enolpyruvylshikimate-3-Phosphate Synthase Overexpression

Fitness is an important trait in weed species that have developed herbicide resistance, including resistance to the popular herbicide glyphosate. Fitness cost is commonly found in weeds with glyphosate resistance, which is caused by target-site mutations. In this study, the vegetative and fecundity fitness traits in a glyphosate-resistant (GR) Eleusine indica population caused by 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression were investigated under glyphosate-free conditions. The results showed that the resistance index of the population resistant (R) to glyphosate compared with that of the population susceptible (WT) to it was approximately 4.0. Furthermore, EPSPS expression level in the R plants was 20.1-82.7 times higher than that in the WT plants. The dry weight of the R population was significantly higher than that of the WT population at the later growth stage after planting; a similar trend was observed for leaf area. In addition, seed production in the R population was 1.4 times higher than that in the WT population. The R and WT populations showed similar maximum germination rates and T₅₀ values. UPLC-MS/MS was performed for the metabolic extracts prepared from the leaves of R and WT populations to address changes in the metabolome. A total of 121 differential metabolites were identified between R and WT individuals. The levels of 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde, which are associated with auxin synthesis, were significantly higher in plants of the R population than in those of the WT population. However, some secondary metabolite levels were slightly lower in the R population than in the WT population. To conclude, in this study, vegetative and fecundity fitness benefits were found in the GR E. indica population. The results of metabolome analysis indicate that the increase in 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde levels may be the result of fitness benefit. Further studies should be conducted to confirm the functions of these metabolites.

Genetic architecture underlying HPPD-inhibitor resistance in a Nebraska Amaranthus tuberculatus population

BACKGROUND

Amaranthus tuberculatus is a problematic weed species in Midwest USA agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB).

RESULTS

Dose-response studies of an F₁ generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F₂ generation determined the trait is moderately heritable (H²  = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12.

CONCLUSIONS

Resistance to HPPD inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.

Glyphosate resistance in Chloris radiata from colombian rice fields involves one target-site mechanism

At present, appearance of herbicide resistant weeds is not new because repeated herbicide treatments per agricultural year/cycle are usual in both perennial and annual crops worldwide. Characterizing resistance mechanisms implied in each herbicide resistant weed is the best tool and the basis to develop integrated weed management (IWM) strategies. The main resistance mechanisms which confer low sensibility to glyphosate in a previously confirmed glyphosate-resistant Chloris radiata population (ChrR), occurring in Colombian rice fields, were characterized. Pure line selection by clone plants showed high resistance levels in ChrR. Comparing with GR50 and LD50 values, ChrR was 9.6 and 10.8 times more resistant with respect to a representative susceptible population (ChrS). The nontarget site mechanisms reduced glyphosate absorption and translocation did not contribute to the glyphosate resistance of the ChrR population. However, enzyme activity assays and DNA sequencing demonstrated that at least one target-site resistance mechanism is involved in such resistance. All ten ChrR plants tested had the amino acid substitution Pro-106-Ser. The results may be crucial to decrease the resistance distribution of C. radiata in Colombia by implementing IWM programs. The change in weed control strategies in rice fields from Colombia must include herbicides with different mode of action from glyphosate and non chemical methods to preserve the useful life of glyphosate longer for weed control in the country.

Point Mutations and Cytochrome P450 Can Contribute to Resistance to ACCase-Inhibiting Herbicides in Three Phalaris Species

Species of Phalaris have historically been controlled by acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides; however, overreliance on herbicides with this mechanism of action has resulted in the selection of resistant biotypes. The resistance to ACCase-inhibiting herbicides was characterized in Phalaris brachystachys, Phalaris minor, and Phalaris paradoxa samples collected from winter wheat fields in northern Iran. Three resistant (R) biotypes, one of each Phalaris species, presented high cross-resistance levels to diclofop-methyl, cycloxydim, and pinoxaden, which belong to the chemical families of aryloxyphenoxypropionates (FOPs), cyclohexanediones (DIMs), and phenylpyrazolines (DENs), respectively. The metabolism of ¹⁴C-diclofop-methyl contributed to the resistance of the P. brachystachys R biotype, while no evidence of herbicide metabolism was found in P. minor or P. paradoxa. ACCase in vitro assays showed that the target sites were very sensitive to FOP, DIM, and DEN herbicides in the S biotypes of the three species, while the R Phalaris spp. biotypes presented different levels of resistance to these herbicides. ACCase gene sequencing confirmed that cross-resistance in Phalaris species was conferred by specific point mutations. Resistance in the P. brachystachys R biotype was due to target site and non-target-site resistance mechanisms, while in P. minor and P. paradoxa, only an altered target site was found.

Identification of the most suitable reference gene for gene expression studies with development and abiotic stress response in Bromus sterilis

Bromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can elucidate the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes was evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used software for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.

Herbicides Tolerance in a Pseudomonas Strain Is Associated With Metabolic Plasticity of Antioxidative Enzymes Regardless of Selection

Agriculture uses many food production chains, and herbicides participate in this process by eliminating weeds through different biochemical strategies. However, herbicides can affect non-target organisms such as bacteria, which can suffer damage if there is no efficient control of reactive oxygen species. It is not clear, according to the literature, whether the efficiency of this control needs to be selected by the presence of xenobiotics. Thus, the Pseudomonas sp. CMA 6.9 strain, collected from biofilms in an herbicide packaging washing tank, was selected for its tolerance to pesticides and analyzed for activities of different antioxidative enzymes against the herbicides Boral^®, absent at the isolation site, and Heat^®, present at the site; both herbicides have the same mode of action, the inhibition of the enzyme protoporphyrinogen oxidase. The strain showed tolerance to both herbicides in doses up to 45 times than those applied in agriculture. The toxicity of these herbicides, which is greater for Boral^®, was assessed by means of oxidative stress indicators, growth kinetics, viability, and amounts of peroxide and malondialdehyde. However, the studied strain showed two characteristic antioxidant response systems for each herbicide: glutathione-s-transferase acting to control malondialdehyde in treatments with Boral^®; and catalase, ascorbate peroxidase, and guaiacol peroxidase in the control of peroxide induced by Heat^®. It is possible that this modulation of the activity of different enzymes independent of previous selection characterizes a system of metabolic plasticity that may be more general in the adaptation of microorganisms in soil and water environments subjected to chemical contaminants. This is relevant to the impact of pesticides on the diversity and abundance of microbial species as well as a promising line of metabolic studies in microbial consortia for use in bioremediation.

An ABCC-type transporter endowing glyphosate resistance in plants

Glyphosate is the most widely used herbicide in world agriculture and for general vegetation control in a wide range of situations. Global and often intensive glyphosate selection of very large weedy plant populations has resulted in widespread glyphosate resistance evolution in populations of many weed species. Here, working with a glyphosate-resistant (GR) Echinochloa colona population that evolved in a Western Australia agricultural field, we identified an ATP-binding cassette (ABC) transporter (EcABCC8) that is consistently up-regulated in GR plants. When expressed in transgenic rice, this EcABCC8 transporter endowed glyphosate resistance. Equally, rice, maize, and soybean overexpressing the EcABCC8 ortholog genes were made resistant to glyphosate. Conversely, CRISPR/Cas9-mediated knockout of the EcABCC8 ortholog gene OsABCC8 increased rice susceptibility to glyphosate. Subcellular localization analysis and quantification of glyphosate cellular levels in treated ABCC8 transgenic rice plants and isolated leaf protoplasts as well as structural modeling support that EcABCC8 is likely a plasma membrane-localized transporter extruding cytoplasmic glyphosate to the apoplast, lowering the cellular glyphosate level. This is a report of a membrane transporter effluxing glyphosate in a GR plant species, and its function is likely conserved in crop plant species.