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Comont D, Crook L, Hull R, Sievernich B, Kevis S, Neve P. The role of interspecific variability and herbicide pre-adaptation in the cinmethylin response of Alopecurus myosuroides. PEST MANAGEMENT SCIENCE 2024; 80:3172-3181. [PMID: 38345468 DOI: 10.1002/ps.8021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Cinmethylin is an inhibitor of plant fatty acid biosynthesis, with in-plant activity caused by its binding to fatty acid thioesterases (FATs). The recent registration of cinmethylin for pre-emergence herbicidal use in the UK represents a new mode-of-action (MOA) for control of the grassweed blackgrass (Alopecurus myosuroides). To date there is little published information on the extent of blackgrass' inter-population variability in sensitivity to cinmethylin, nor on any potential effect of existing non-target-site resistance (NTSR) mechanisms on cinmethylin efficacy. RESULTS Here we present a study of variability in cinmethylin sensitivity amongst 97 UK blackgrass populations. We demonstrate that under controlled conditions, a UK field-rate dose of 500 g ha-1 provides effective control of the tested populations. Nevertheless, we reveal significant inter-population variability at doses below this rate, with populations previously characterised as strongly NTSR displaying the lowest sensitivity to cinmethylin. Assessment of paired resistant 'R' and sensitive 'S' lines from standardised genetic backgrounds confirms that selection for NTSR to the acetyl-CoA-carboxylase inhibitor fenoxaprop, and the microtubule assembly inhibitor pendimethalin, simultaneously results in reduced sensitivity to cinmethylin at doses below 500 g ha-1. Whilst we find no resistance to the field-rate dose, we reveal that cinmethylin sensitivity can be further reduced through experimental selection with cinmethylin. CONCLUSION Cinmethylin therefore represents a much-needed further MOA for blackgrass control, but needs to be carefully managed within a resistance monitoring and integrated weed management (IWM) framework to maximise the effective longevity of this compound. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- David Comont
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Laura Crook
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Richard Hull
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Bernd Sievernich
- Technical Project Management Europe, Agricultural Solutions BASF SE, Limburgerhof, Germany
| | - Stuart Kevis
- Business Development, Agricultural Solutions UK, BASF Plc, Stockport, UK
| | - Paul Neve
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
- Department of Plant and Environmental Sciences, Section for Crop Sciences, University of Copenhagen, Taastrup, Denmark
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2
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Lowe C, Onkokesung N, Goldberg A, Beffa R, Neve P, Edwards R, Comont D. RNA and protein biomarkers for detecting enhanced metabolic resistance to herbicides mesosulfuron-methyl and fenoxaprop-ethyl in black-grass (Alopecurus myosuroides). PEST MANAGEMENT SCIENCE 2024; 80:2539-2551. [PMID: 38375975 DOI: 10.1002/ps.7960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND The evolution of non-target site resistance (NTSR) to herbicides leads to a significant reduction in herbicide control of agricultural weed species. Detecting NTSR in weed populations prior to herbicide treatment would provide valuable information for effective weed control. While not all NTSR mechanisms have been fully identified, enhanced metabolic resistance (EMR) is one of the better studied, conferring tolerance through increased herbicide detoxification. Confirming EMR towards specific herbicides conventionally involves detecting metabolites of the active herbicide molecule in planta, but this approach is time-consuming and requires access to well-equipped laboratories. RESULTS In this study, we explored the potential of using molecular biomarkers to detect EMR before herbicide treatment in black-grass (Alopecurus myosuroides). We tested the reliability of selected biomarkers to predict EMR and survival after herbicide treatments in both reference and 27 field-derived black-grass populations collected from sites across the UK. The combined analysis of the constitutive expression of biomarkers and metabolism studies confirmed three proteins, namely, AmGSTF1, AmGSTU2 and AmOPR1, as differential biomarkers of EMR toward the herbicides fenoxaprop-ethyl and mesosulfuron in black-grass. CONCLUSION Our findings demonstrate that there is potential to use molecular biomarkers to detect EMR toward specific herbicides in black-grass without reference to metabolism analysis. However, biomarker development must include testing at both transcript and protein levels in order to be reliable indicators of resistance. This work is a first step towards more robust resistance biomarker development, which could be expanded into other herbicide chemistries for on-farm testing and monitoring EMR in uncharacterised black-grass populations. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Claudia Lowe
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Nawaporn Onkokesung
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Alina Goldberg
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Roland Beffa
- Senior Scientific Consultant, Liederbach, Germany
| | - Paul Neve
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Robert Edwards
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - David Comont
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
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3
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Harrison C, Noleto-Dias C, Ruvo G, Hughes DJ, Smith DP, Mead A, Ward JL, Heuer S, MacGregor DR. The mechanisms behind the contrasting responses to waterlogging in black-grass ( Alopecurus myosuroides) and wheat ( Triticum aestivum). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23193. [PMID: 38417910 DOI: 10.1071/fp23193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/07/2024] [Indexed: 03/01/2024]
Abstract
Black-grass (Alopecurus myosuroides ) is one of the most problematic agricultural weeds of Western Europe, causing significant yield losses in winter wheat (Triticum aestivum ) and other crops through competition for space and resources. Previous studies link black-grass patches to water-retaining soils, yet its specific adaptations to these conditions remain unclear. We designed pot-based waterlogging experiments to compare 13 biotypes of black-grass and six cultivars of wheat. These showed that wheat roots induced aerenchyma when waterlogged whereas aerenchyma-like structures were constitutively present in black-grass. Aerial biomass of waterlogged wheat was smaller, whereas waterlogged black-grass was similar or larger. Variability in waterlogging responses within and between these species was correlated with transcriptomic and metabolomic changes in leaves of control or waterlogged plants. In wheat, transcripts associated with regulation and utilisation of phosphate compounds were upregulated and sugars and amino acids concentrations were increased. Black-grass biotypes showed limited molecular responses to waterlogging. Some black-grass amino acids were decreased and one transcript commonly upregulated was previously identified in screens for genes underpinning metabolism-based resistance to herbicides. Our findings provide insights into the different waterlogging tolerances of these species and may help to explain the previously observed patchiness of this weed's distribution in wheat fields.
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Affiliation(s)
- Christian Harrison
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire, UK
| | - Clarice Noleto-Dias
- Rothamsted Research, Plant Sciences for the Bioeconomy, Harpenden, Hertfordshire, UK
| | - Gianluca Ruvo
- Rothamsted Research, Plant Sciences for the Bioeconomy, Harpenden, Hertfordshire, UK
| | - David J Hughes
- Rothamsted Research, Intelligent Data Ecosystems, Harpenden, Hertfordshire, UK
| | - Daniel P Smith
- Rothamsted Research, Intelligent Data Ecosystems, Harpenden, Hertfordshire, UK
| | - Andrew Mead
- Rothamsted Research, Intelligent Data Ecosystems, Harpenden, Hertfordshire, UK
| | - Jane L Ward
- Rothamsted Research, Plant Sciences for the Bioeconomy, Harpenden, Hertfordshire, UK
| | - Sigrid Heuer
- International Consultant Crop Improvement and Food Security, Harpenden, UK
| | - Dana R MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire, UK
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4
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Font Farre M, Brown D, König M, Killinger BJ, Kaschani F, Kaiser M, Wright AT, Burton J, van der Hoorn RAL. Glutathione Transferase Photoaffinity Labeling Displays GST Induction by Safeners and Pathogen Infection. PLANT & CELL PHYSIOLOGY 2024; 65:128-141. [PMID: 37924215 PMCID: PMC10799724 DOI: 10.1093/pcp/pcad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Glutathione transferases (GSTs) represent a large and diverse enzyme family involved in the detoxification of small molecules by glutathione conjugation in crops, weeds and model plants. In this study, we introduce an easy and quick assay for photoaffinity labeling of GSTs to study GSTs globally in various plant species. The small-molecule probe contains glutathione, a photoreactive group and a minitag for coupling to reporter tags via click chemistry. Under UV irradiation, this probe quickly and robustly labels GSTs in crude protein extracts of different plant species. Purification and mass spectrometry (MS) analysis of labeled proteins from Arabidopsis identified 10 enriched GSTs from the Phi(F) and Tau(U) classes. Photoaffinity labeling of GSTs demonstrated GST induction in wheat seedlings upon treatment with safeners and in Arabidopsis leaves upon infection with avirulent bacteria. Treatment of Arabidopsis with salicylic acid (SA) analog benzothiadiazole (BTH) induces GST labeling independent of NPR1, the master regulator of SA. Six Phi- and Tau-class GSTs that are induced upon BTH treatment were identified, and their labeling was confirmed upon transient overexpression. These data demonstrate that GST photoaffinity labeling is a useful approach to studying GST induction in crude extracts of different plant species upon different types of stress.
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Affiliation(s)
- Maria Font Farre
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Daniel Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, Oxfordshire OX1 3TA, UK
| | - Maurice König
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Brian J Killinger
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen 45141, Germany
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen 45141, Germany
| | - Aaron T Wright
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
- Department of Biology, Baylor University, Waco, TX 76798, USA
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Jonathan Burton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, Oxfordshire OX1 3TA, UK
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5
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Sen MK, Bhattacharya S, Bharati R, Hamouzová K, Soukup J. Comprehensive insights into herbicide resistance mechanisms in weeds: a synergistic integration of transcriptomic and metabolomic analyses. FRONTIERS IN PLANT SCIENCE 2023; 14:1280118. [PMID: 37885667 PMCID: PMC10598704 DOI: 10.3389/fpls.2023.1280118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
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.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Suchdol, Czechia
| | - Soham Bhattacharya
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Suchdol, Czechia
| | - Rohit Bharati
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Suchdol, Czechia
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Suchdol, Czechia
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Suchdol, Czechia
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6
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Fu W, MacGregor DR, Comont D, Saski CA. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass ( Alopecurus myosuroides) Populations. Genes (Basel) 2023; 14:1905. [PMID: 37895254 PMCID: PMC10606437 DOI: 10.3390/genes14101905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
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Affiliation(s)
- Wangfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Dana R. MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - David Comont
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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7
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Parcharidou E, Dücker R, Zöllner P, Ries S, Orru R, Beffa R. Recombinant glutathione transferases from flufenacet-resistant black-grass (Alopecurus myosuroides Huds.) form different flufenacet metabolites and differ in their interaction with pre- and post-emergence herbicides. PEST MANAGEMENT SCIENCE 2023; 79:3376-3386. [PMID: 37132078 DOI: 10.1002/ps.7523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Black-grass (Alopecurus myosuroides Huds.) has become a problematic weed in cereals in Europe. Besides resistance to post-emergent herbicides becoming increasingly widespread, enhanced metabolism of inhibitors of the synthesis of very-long-chain fatty acids (VLCFAs), such as flufenacet, is evolving. Yet, cross-resistance patterns and evolution of this resistance remains poorly understood. RESULTS The cDNA sequences of five glutathione transferases (GSTs) upregulated in flufenacet resistant black-grass were identified and used for recombinant protein expression. Moderate to slow detoxification of flufenacet was verified for all candidate GSTs expressed in E. coli, and the most active protein produced flufenacet-alcohol instead of a glutathione conjugate, in the presence of reduced glutathione (GSH). Moreover, cross-resistance to other VLCFA-inhibitors e.g., acetochlor and pyroxasulfone and the ACCase inhibitor fenoxaprop was verified in vitro. Various other herbicides of different modes of action including VLCFA-inhibitors were not detoxified by the candidate GSTs. CONCLUSIONS As several in planta upregulated GSTs detoxified flufenacet in vitro, the shift in sensitivity observed in black-grass populations, is likely a result of an additive effect. The polygenic character and the relatively low turnover rate of the individual GSTs may explain the slow evolution of flufenacet resistance. In addition, flufenacet resistance was accompanied by cross-resistance with some, but not all, herbicides of the same mode of action, and furthermore to the ACCase inhibitor fenoxaprop-ethyl. Hence, not only the rotation of herbicide modes of action, but also of individual active ingredients is important for resistance management. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Evlampia Parcharidou
- Division of Plant Pathology and Crop Protection, Georg-August University Göttingen, Göttingen, Germany
| | - Rebecka Dücker
- Division of Plant Pathology and Crop Protection, Georg-August University Göttingen, Göttingen, Germany
| | - Peter Zöllner
- Bayer AG, CropScience Division, Industrial Park Höchst, Frankfurt am Main, Germany
| | - Susanne Ries
- Bayer AG, CropScience Division, Industrial Park Höchst, Frankfurt am Main, Germany
| | - Roberto Orru
- Bayer AG, CropScience Division, Industrial Park Höchst, Frankfurt am Main, Germany
| | - Roland Beffa
- Senior Scientist Consultant, Liederbach am Taunus, Germany
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8
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Zhang L, Wang W, Du Y, Deng Y, Bai T, Ji M. Multiple resistance of Echinochloa phyllopogon to synthetic auxin, ALS-, and ACCase-inhibiting herbicides in Northeast China. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 193:105450. [PMID: 37248019 DOI: 10.1016/j.pestbp.2023.105450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/31/2023]
Abstract
Echinochloa phyllopogon is a self-pollinating allotetraploid weed and a serious threat to global rice production. One sensitive and three multiple-resistant populations collected from two provinces of Northeast China were used to analyze the mechanism of multiple resistance of E. phyllopogon to penoxsulam, metamifop, and quinclorac. Compared with the sensitive population LN12, LN1 showed higher resistance to these three herbicides; LN24 showed medium resistance to penoxsulam and metamifop and higher resistance to quinclorac (274-fold); HLJ4 showed low resistance to penoxsulam and high resistance to metamifop and quinclorac. Target sequence analysis showed no mutations in acetolactate synthase or acetyl-CoA carboxylase genes. In-vitro enzyme activity analysis showed that the activity of the target enzyme of multiple herbicide-resistant populations was similar to that of the sensitive population. The P450 inhibitor, malathion, noticeably increased the sensitivity of LN1, LN24, and HLJ4 to penoxsulam, LN1 to metamifop, and HLJ4 to quinclorac. Under all four treatments, the GSTs activities of resistant and sensitive populations showed an increasing trend from day 1 to day 5, but the sensitivity and activity of GSTs were higher in the multiple-resistant population than that in the sensitive population LN12. This study identified the development of multiple-resistant E. phyllopogon populations that pose a serious threat to rice production in rice fields in Northeast China, preliminarily confirming that multiple-resistance was likely due to non-target-site resistance mechanisms. These populations of E. phyllopogon are likely to be more difficult to control.
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Affiliation(s)
- Lulu Zhang
- Shenyang Agricultural University, College of Plant Protection, Shenyang, Liaoning 110866, China
| | - Weijing Wang
- Agricultural and Rural Bureau of Caofeidian District, Tangshan, Hebei 063299, China
| | - Ying Du
- Shenyang Agricultural University, College of Plant Protection, Shenyang, Liaoning 110866, China
| | - Yunyan Deng
- Shenyang Agricultural University, College of Plant Protection, Shenyang, Liaoning 110866, China
| | - Tianlang Bai
- Shenyang Agricultural University, College of Plant Protection, Shenyang, Liaoning 110866, China
| | - Mingshan Ji
- Shenyang Agricultural University, College of Plant Protection, Shenyang, Liaoning 110866, China.
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9
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Goldberg-Cavalleri A, Onkokesung N, Franco-Ortega S, Edwards R. ABC transporters linked to multiple herbicide resistance in blackgrass ( Alopecurus myosuroides). FRONTIERS IN PLANT SCIENCE 2023; 14:1082761. [PMID: 37008473 PMCID: PMC10063862 DOI: 10.3389/fpls.2023.1082761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Enhanced detoxification is a prominent mechanism protecting plants from toxic xenobiotics and endows resistance to diverse herbicide chemistries in grass weeds such as blackgrass (Alopecurus myosuroides). The roles of enzyme families which impart enhanced metabolic resistance (EMR) to herbicides through hydroxylation (phase 1 metabolism) and/or conjugation with glutathione or sugars (phase 2) have been well established. However, the functional importance of herbicide metabolite compartmentalisation into the vacuole as promoted by active transport (phase 3), has received little attention as an EMR mechanism. ATP-binding cassette (ABC) transporters are known to be important in drug detoxification in fungi and mammals. In this study, we identified three distinct C-class ABCCs transporters namely AmABCC1, AmABCC2 and AmABCC3 in populations of blackgrass exhibiting EMR and resistance to multiple herbicides. Uptake studies with monochlorobimane in root cells, showed that the EMR blackgrass had an enhanced capacity to compartmentalize fluorescent glutathione-bimane conjugated metabolites in an energy-dependent manner. Subcellular localisation analysis using transient expression of GFP-tagged AmABCC2 assays in Nicotiana demonstrated that the transporter was a membrane bound protein associated with the tonoplast. At the transcript level, as compared with herbicide sensitive plants, AmABCC1 and AmABCC2 were positively correlated with EMR in herbicide resistant blackgrass being co-expressed with AmGSTU2a, a glutathione transferase (GST) involved in herbicide detoxification linked to resistance. As the glutathione conjugates generated by GSTs are classic ligands for ABC proteins, this co-expression suggested AmGSTU2a and the two ABCC transporters delivered the coupled rapid phase 2/3 detoxification observed in EMR. A role for the transporters in resistance was further confirmed in transgenic yeast by demonstrating that the expression of either AmABCC1 or AmABCC2, promoted enhanced tolerance to the sulfonylurea herbicide, mesosulfuron-methyl. Our results link the expression of ABCC transporters to enhanced metabolic resistance in blackgrass through their ability to transport herbicides, and their metabolites, into the vacuole.
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10
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Cai L, Comont D, MacGregor D, Lowe C, Beffa R, Neve P, Saski C. The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance. THE NEW PHYTOLOGIST 2023; 237:1891-1907. [PMID: 36457293 PMCID: PMC10108218 DOI: 10.1111/nph.18655] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 11/23/2022] [Indexed: 05/31/2023]
Abstract
Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.
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Affiliation(s)
- Lichun Cai
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - David Comont
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Dana MacGregor
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Claudia Lowe
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Roland Beffa
- Bayer Crop SciencesIndustriepark Höchst65926Frankfurt am MainGermany
- Königsteiner Weg 465835LiederbachGermany
| | - Paul Neve
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
- Department of Plant and Environmental SciencesUniversity of CopenhagenHøjbakkegård Allé 13Tåstrup2630Denmark
| | - Christopher Saski
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
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11
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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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12
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Ioannou E, Papageorgiou AC, Labrou NE. Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops. Int J Mol Sci 2022; 23:ijms23137469. [PMID: 35806486 PMCID: PMC9267659 DOI: 10.3390/ijms23137469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
The extensive application of herbicides in crop cultivation has indisputably led to the emergence of weed populations characterized by multiple herbicide resistance (MHR). This phenomenon is associated with the enhanced metabolism and detoxifying ability of endogenous enzymes, such as phi class glutathione transferases (GSTFs). In the present work, a library of mutant GSTFs was created by in vitro directed evolution via DNA shuffling. Selected gstf genes from the weeds Alopecurus myosuroides and Lolium rigidum, and the cereal crops Triticum durum and Hordeum vulgare were recombined to forge a library of novel chimeric GSTFs. The library was activity screened and the best-performing enzyme variants were purified and characterized. The work allowed the identification of enzyme variants that exhibit an eight-fold improvement in their catalytic efficiency, higher thermal stability (8.3 °C) and three-times higher inhibition sensitivity towards the herbicide butachlor. The crystal structures of the best-performing enzyme variants were determined by X-ray crystallography. Structural analysis allowed the identification of specific structural elements that are responsible for kcat regulation, thermal stability and inhibition potency. These improved novel enzymes hold the potential for utilization in biocatalysis and green biotechnology applications. The results of the present work contribute significantly to our knowledge of the structure and function of phi class plant GSTs and shed light on their involvement in the mechanisms of MHR.
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Affiliation(s)
- Elisavet Ioannou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece;
| | | | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece;
- Correspondence:
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13
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Comont D, MacGregor DR, Crook L, Hull R, Nguyen L, Freckleton RP, Childs DZ, Neve P. Dissecting weed adaptation: Fitness and trait correlations in herbicide-resistant Alopecurus myosuroides. PEST MANAGEMENT SCIENCE 2022; 78:3039-3050. [PMID: 35437938 PMCID: PMC9324217 DOI: 10.1002/ps.6930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Unravelling the genetic architecture of non-target-site resistance (NTSR) traits in weed populations can inform questions about the inheritance, trade-offs and fitness costs associated with these traits. Classical quantitative genetics approaches allow study of the genetic architecture of polygenic traits even where the genetic basis of adaptation remains unknown. These approaches have the potential to overcome some of the limitations of previous studies into the genetics and fitness of NTSR. RESULTS Using a quantitative genetic analysis of 400 pedigreed Alopecurus myosuroides seed families from nine field-collected populations, we found strong heritability for resistance to the acetolactate synthase and acetyl CoA carboxylase inhibitors (h2 = 0.731 and 0.938, respectively), and evidence for shared additive genetic variance for resistance to these two different herbicide modes of action, rg = 0.34 (survival), 0.38 (biomass). We find no evidence for genetic correlations between life-history traits and herbicide resistance, indicating that resistance to these two modes of action is not associated with large fitness costs in blackgrass. We do, however, demonstrate that phenotypic variation in plant flowering characteristics is heritable, h2 = 0.213 (flower height), 0.529 (flower head number), 0.449 (time to flowering) and 0.372 (time to seed shed), demonstrating the potential for adaptation to other nonchemical management practices (e.g. mowing of flowering heads) now being adopted for blackgrass control. CONCLUSION These results highlight that quantitative genetics can provide important insight into the inheritance and genetic architecture of NTSR, and can be used alongside emerging molecular techniques to better understand the evolutionary and fitness landscape of herbicide resistance. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- David Comont
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
| | - Dana R MacGregor
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
- Department of BiosciencesUniversity of DurhamDurhamUK
| | - Laura Crook
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
| | - Richard Hull
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
| | - Lieselot Nguyen
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
| | - Robert P Freckleton
- Department of Animal and Plant SciencesUniversity of SheffieldSouth YorkshireUK
| | - Dylan Z Childs
- Department of Animal and Plant SciencesUniversity of SheffieldSouth YorkshireUK
| | - Paul Neve
- Department of Biointeractions and Crop ProtectionRothamsted Research, HarpendenHertfordshireUK
- Department of Plant and Environmental Sciences, Section for Crop SciencesUniversity of CopenhagenTaastrupDenmark
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14
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Chandra S, Leon RG. Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots. Genes (Basel) 2022; 13:genes13071171. [PMID: 35885954 PMCID: PMC9316059 DOI: 10.3390/genes13071171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/06/2023] Open
Abstract
Herbicides are key weed-control tools, but their repeated use across large areas has favored the evolution of herbicide resistance. Although target-site has been the most prevalent and studied type of resistance, non-target-site resistance (NTSR) is increasing. However, the genetic factors involved in NTSR are widely unknown. In this study, four gene groups encoding putative NTSR enzymes, namely, cytochrome-P450, glutathione-S-transferase (GST), uridine 5'-diphospho-glucuronosyltransferase (UDPGT), and nitronate monooxygenase (NMO) were analyzed. The monocot and dicot gene sequences were downloaded from publicly available databases. Phylogenetic trees revealed that most of the CYP450 resistance-related sequences belong to CYP81 (5), and in GST, most of the resistance sequences belonged to GSTU18 (9) and GSTF6 (8) groups. In addition, the study of upstream promoter sequences of these NTSR genes revealed stress-related cis-regulatory motifs, as well as eight transcription factor binding sites (TFBS) were identified. The discovered TFBS were commonly present in both monocots and dicots, and the identified motifs are known to play key roles in countering abiotic stress. Further, we predicted the 3D structure for the resistant CYP450 and GST protein and identified the substrate recognition site through the homology approach. Our description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.
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Affiliation(s)
- Saket Chandra
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ramon G. Leon
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
- Genetic Engineering and Society Center, Center for Environmental Farming Systems, North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: ; Tel.: +1-919-515-5328
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15
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Torra J, Osuna MD, Merotto A, Vila-Aiub M. Editorial: Multiple Herbicide-Resistant Weeds and Non-target Site Resistance Mechanisms: A Global Challenge for Food Production. FRONTIERS IN PLANT SCIENCE 2021; 12:763212. [PMID: 34777445 PMCID: PMC8581628 DOI: 10.3389/fpls.2021.763212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/29/2021] [Indexed: 05/07/2023]
Affiliation(s)
- Joel Torra
- Department d'Hortofructicultura, Botànica i Jardineria, Agrotecnio-CERCA Center, Universitat de Lleida, Lleida, Spain
| | - María Dolores Osuna
- Center for Scientific and Technological Research of Extremadura (CICYTEX), Agrarian Research Center “Finca La Orden” Valdesequera, Badajoz, Spain
| | - Aldo Merotto
- Department of Crop Science, Faculty of Agronomy, Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, Brazil
| | - Martin Vila-Aiub
- Department of Ecology, IFEVA -CONICET, Faculty of Agronomy, University of Buenos Aires (UBA), Buenos Aires, Argentina
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16
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Kaundun SS. Syngenta's contribution to herbicide resistance research and management. PEST MANAGEMENT SCIENCE 2021; 77:1564-1571. [PMID: 32893405 PMCID: PMC7984027 DOI: 10.1002/ps.6072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/18/2020] [Accepted: 09/07/2020] [Indexed: 05/03/2023]
Abstract
The evolution of weed resistance to herbicides is an ever-increasing problem that affects crop yield and food production. In Syngenta, we believe that this difficult and complex issue can be most efficiently addressed through a deep understanding of the evolutionary dynamics and mechanism of resistance. A profound knowledge of resistance is key to developing the next generation of resistance-breaking compounds with existing or novel herbicide sites of action. We use a multidisciplinary laboratory-based, glasshouse and field biology approach to study herbicide resistance and provide strong science-based solutions to delay the onset and manage resistance. We have developed and implemented simple early-season resistance detection methods to allow farmers make an informed decision for effective weed control. We have built mechanistic, individual-based computer models to design profitable, long-term sustainable weed management programs. Our zero tolerance approaches employ herbicides with different sites of action, applied in mixtures and sequences, to minimise the risk of resistance evolution. Weeds are targeted at the right growth stage with optimal herbicide formulation and spray technology for maximising weed control and depleting the seed bank. We are promoting the use of competitive crop varieties and other nonchemical methods for an integrated weed management strategy. We have a global web of external collaborations for studying and managing herbicide resistance. We are committed to farmers' education and training on herbicide resistance, and regularly share our methods and findings via conferences and peer-reviewed scientific publications for the benefit of the wider weed science community and field practitioners. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shiv Shankhar Kaundun
- Herbicide Bioscience, SyngentaJealott's Hill International Research CentreBerkshireUK
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17
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Sen MK, Hamouzová K, Mikulka J, Bharati R, Košnarová P, Hamouz P, Roy A, Soukup J. Enhanced metabolism and target gene overexpression confer resistance against acetolactate synthase-inhibiting herbicides in Bromus sterilis. PEST MANAGEMENT SCIENCE 2021; 77:2122-2128. [PMID: 33332713 DOI: 10.1002/ps.6241] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Intensive application of acetolactate synthase (ALS)-inhibiting herbicides has resulted in herbicide-resistance in many weeds, including Bromus sterilis. The present study was conducted to identify the mechanisms conferring resistance to ALS-inhibiting herbicides in a Bromus sterilis biotype. RESULTS Dose-response studies revealed the resistant biotype to be 288 times less sensitive to pyroxsulam than the susceptible biotype. Furthermore, experiment with a single-dose, proved this biotype was also cross-resistant to propoxycarbazone, iodosulfuron plus mesosulfuron and sulfosulfuron. Prior treatment with malathion, a known inhibitor of cytochrome P450s, reduced the level of resistance to pyroxsulam. No mutations were detected from the partial ALS gene sequencing. Flow cytometry and chromosome counting rejected ploidy level variation between the susceptible and resistant biotypes. Relative copy number variation ruled out gene amplification. Quantitative real-time polymerase chain reaction (PCR) detected a significant difference in ALS gene expression between the susceptible and resistant biotypes. CONCLUSIONS Target gene overexpression and enhanced metabolism by cytochrome P450s are likely mechanisms of resistance to pyroxsulam in Bromus sterilis. The current findings highlight the need to monitor additional brome populations for herbicide resistance in Europe and endorse the need for alternate herbicides in integrated weed management to delay the possible evolution of herbicide resistance in these species. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jakub Mikulka
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavlina Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hamouz
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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18
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Franco-Ortega S, Goldberg-Cavalleri A, Walker A, Brazier-Hicks M, Onkokesung N, Edwards R. Non-target Site Herbicide Resistance Is Conferred by Two Distinct Mechanisms in Black-Grass ( Alopecurus myosuroides). FRONTIERS IN PLANT SCIENCE 2021; 12:636652. [PMID: 33747015 PMCID: PMC7966817 DOI: 10.3389/fpls.2021.636652] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/26/2021] [Indexed: 05/31/2023]
Abstract
Non-target site resistance (NTSR) to herbicides in black-grass (Alopecurus myosuroides) results in enhanced tolerance to multiple chemistries and is widespread in Northern Europe. To help define the underpinning mechanisms of resistance, global transcriptome and biochemical analysis have been used to phenotype three NTSR black-grass populations. These comprised NTSR1 black-grass from the classic Peldon field population, which shows broad-ranging resistance to post-emergence herbicides; NTSR2 derived from herbicide-sensitive (HS) plants repeatedly selected for tolerance to pendimethalin; and NTSR3 selected from HS plants for resistance to fenoxaprop-P-ethyl. NTSR in weeds is commonly associated with enhanced herbicide metabolism catalyzed by glutathione transferases (GSTs) and cytochromes P450 (CYPs). As such, the NTSR populations were assessed for their ability to detoxify chlorotoluron, which is detoxified by CYPs and fenoxaprop-P-ethyl, which is acted on by GSTs. As compared with HS plants, enhanced metabolism toward both herbicides was determined in the NTSR1 and NTSR2 populations. In contrast, the NTSR3 plants showed no increased detoxification capacity, demonstrating that resistance in this population was not due to enhanced metabolism. All resistant populations showed increased levels of AmGSTF1, a protein functionally linked to NTSR and enhanced herbicide metabolism. Enhanced AmGSTF1 was associated with increased levels of the associated transcripts in the NTSR1 and NTSR2 plants, but not in NTSR3, suggestive of both pre- and post-transcriptional regulation. The related HS, NTSR2, and NTSR3 plants were subject to global transcriptome sequencing and weighted gene co-expression network analysis to identify modules of genes with coupled regulatory functions. In the NTSR2 plants, modules linked to detoxification were identified, with many similarities to the transcriptome of NTSR1 black-grass. Critical detoxification genes included members of the CYP81A family and tau and phi class GSTs. The NTSR2 transcriptome also showed network similarities to other (a)biotic stresses of plants and multidrug resistance in humans. In contrast, completely different gene networks were activated in the NTSR3 plants, showing similarity to the responses to cold, osmotic shock and fungal infection determined in cereals. Our results demonstrate that NTSR in black-grass can arise from at least two distinct mechanisms, each involving complex changes in gene regulatory networks.
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19
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Georgakis N, Poudel N, Vlachakis D, Papageorgiou AC, Labrou NE. Phi class glutathione transferases as molecular targets towards multiple-herbicide resistance: Inhibition analysis and pharmacophore design. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:342-352. [PMID: 33257232 DOI: 10.1016/j.plaphy.2020.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Multiple-herbicide resistance (MHR) is a global threat to weed control in cereal crops. MHR weeds express a specific phi class glutathione transferase (MHR-GSTF) that confers resistance against multiple herbicides and therefore represents a promising target against MHR weeds. Kinetics inhibition analysis of MHR-GSTFs from grass weeds Lolium rigidum (LrGSTF) Alopecurus myosuroides (AmGSTF) and crops Hordeum vulgare (HvGSTF) and Triticum aestivum (TaGSTF) allowed the identification of the acetanilide herbicide butachlor as a potent and selective inhibitor towards MHR-GSTFs. Also, butachlor is a stronger inhibitor for LrGSTF and AmGSTF compared to HvGSTF and TaGSTF from crops. The crystal structure of LrGSTF was determined at 1.90 Å resolution in complex with the inhibitor S-(4-nitrobenzyl)glutathione. A specific 3D pharmacophore targeting the MHR-GSTFs was designed and used to identify structural elements important for potent and selective inhibition. Structural analysis of GSTFs revealed a decisive role of conserved Tyr118 in ligand binding and pharmacophore design. Its positioning is dependent on an outer patch of adjacent residues that span from position 132 to 134 which are similar for both LrGSTF and AmGSTF but different in HvGSTF and TaGSTF. The results presented here provide new knowledge that may be adopted to cope with MHR weeds.
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Affiliation(s)
- Nikolaos Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR, 11855, Athens, Greece
| | - Nirmal Poudel
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, 20521, Finland
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR, 11855, Athens, Greece
| | | | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR, 11855, Athens, Greece.
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20
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Davies LR, Onkokesung N, Brazier-Hicks M, Edwards R, Moss S. Detection and characterization of resistance to acetolactate synthase inhibiting herbicides in Anisantha and Bromus species in the United Kingdom. PEST MANAGEMENT SCIENCE 2020; 76:2473-2482. [PMID: 32061023 DOI: 10.1002/ps.5788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Anisantha and Bromus spp. are widespread and difficult to control, potentially due to the evolution of herbicide resistance. In this study, UK populations of four brome species have been tested for the early development of resistance to acetolactate synthase (ALS)-inhibiting herbicides commonly used in their control. RESULTS Glasshouse assays confirmed reduced sensitivity to ALS-inhibiting herbicides in single populations of A. diandra, B. commutatus and B. secalinus, and in three populations of A. sterilis. By contrast, all 60 brome populations tested were sensitive to the ACCase-inhibiting herbicide propaquizafop and glyphosate. Dose-response with two ALS herbicides showed broad-ranging resistance in the A. diandra, A. sterilis and B. commutatus populations. In the B. commutatus population, this was associated with a point mutation in the ALS enzyme conferring target site resistance (TSR). Additionally, resistant populations of A. sterilis and B. commutatus populations contained enhanced amounts of an orthologue of the glutathione transferase phi (F) class 1 (GSTF1) protein, a functional biomarker of nontarget site resistance (NTSR) in Alopecurus myosuroides. There was further evidence of NTSR as these plants also demonstrated an enhanced capacity to detoxify herbicides. CONCLUSION This study confirms the evolution of resistance to ALS inhibiting herbicides in brome species in the UK by mechanisms consistent with the evolution of both TSR and NTSR. These findings point to the need for increased vigilance in detecting and mitigating against the evolution of herbicide resistance in brome species in Northern Europe. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Laura R Davies
- Crop Protection department, Weed biology, ADAS Boxworth, Boxworth, UK
| | - Nawaporn Onkokesung
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Melissa Brazier-Hicks
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Robert Edwards
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Stephen Moss
- Independent consultant, Stephen Moss Consulting, Harpenden, UK
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21
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Comont D, Lowe C, Hull R, Crook L, Hicks HL, Onkokesung N, Beffa R, Childs DZ, Edwards R, Freckleton RP, Neve P. Evolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management. Nat Commun 2020; 11:3086. [PMID: 32555156 PMCID: PMC7303185 DOI: 10.1038/s41467-020-16896-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Intense selection by pesticides and antibiotics has resulted in a global epidemic of evolved resistance. In agriculture and medicine, using mixtures of compounds from different classes is widely accepted as optimal resistance management. However, this strategy may promote the evolution of more generalist resistance mechanisms. Here we test this hypothesis at a national scale in an economically important agricultural weed: blackgrass (Alopecurus myosuroides), for which herbicide resistance is a major economic issue. Our results reveal that greater use of herbicide mixtures is associated with lower levels of specialist resistance mechanisms, but higher levels of a generalist mechanism implicated in enhanced metabolism of herbicides with diverse modes of action. Our results indicate a potential evolutionary trade-off in resistance management, whereby attempts to reduce selection for specialist resistance traits may promote the evolution of generalist resistance. We contend that where specialist and generalist resistance mechanisms co-occur, similar trade-offs will be evident, calling into question the ubiquity of resistance management based on mixtures and combination therapies. Mixtures of antibiotics or pesticides can help reduce the evolution of resistance to individual compounds. Here, Comont et al. show that in blackgrass, an important agricultural weed, herbicide mixtures do reduce specialized resistance but instead can select for a generalized resistance mechanism.
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Affiliation(s)
- David Comont
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Claudia Lowe
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Richard Hull
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Laura Crook
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Helen L Hicks
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, S10 2TN, UK.,School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, NG25 0QF, UK
| | - Nawaporn Onkokesung
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Roland Beffa
- Bayer Crop Science, Weed Resistance Research, 65926, Frankfurt, Germany
| | - Dylan Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, S10 2TN, UK
| | - Robert Edwards
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Robert P Freckleton
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, S10 2TN, UK
| | - Paul Neve
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.,Agriculture & Horticulture Development Board, Stoneleigh Park, Kenilworth, CV8 2TL, UK
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Georgakis N, Poudel N, Papageorgiou AC, Labrou NE. Comparative structural and functional analysis of phi class glutathione transferases involved in multiple-herbicide resistance of grass weeds and crops. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:266-276. [PMID: 32088578 DOI: 10.1016/j.plaphy.2020.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Multiple-herbicide resistant (MHR) weeds are a global problem and a looming threat to weed control in crops. MHR weeds express a specific phi class glutathione transferase (MHR-GSTF) which seems to contribute to herbicide resistance. The present work aims to investigate the structure and catalytic properties of the MHR-GSTFs from different grass weeds and crops (Alopecurus myosuroides, Lolium rigidum, Hordeum vulgare, Triticum aestivum). Recombinant MHR-GSTFs were expressed in E. coli and purified by affinity chromatography. Kinetic analysis of substrate specificity using a range of thiol substrates and xenobiotic compounds suggested that all enzymes display a broad range of specificity and are capable of detoxifying major stress-induced toxic products. Notably, all tested enzymes exhibited high activity towards organic hydroperoxides. The crystal structure of MHR-GSTF from Alopecurus myosuroides (AmGSTF) was determined by molecular replacement at 1.33 Å resolution. The enzyme was resolved with bound glutathione sulfenic acid (GSOH) at the G-site and succinic acid at the H-site. The enzyme shows conserved structural features compared to other Phi class GSTs. However, some differences were observed at the C-terminal helix H9 that may affect substrate specificity. The structural and functional features of AmGSTF were compared with those of the homologue crop enzymes (HvGSTF and TaGSTF) and discussed in light of their contribution to the MHR mechanism.
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Affiliation(s)
- Nikolaos Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nirmal Poudel
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, 20521, Finland
| | | | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
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Comont D, Hicks H, Crook L, Hull R, Cocciantelli E, Hadfield J, Childs D, Freckleton R, Neve P. Evolutionary epidemiology predicts the emergence of glyphosate resistance in a major agricultural weed. THE NEW PHYTOLOGIST 2019; 223:1584-1594. [PMID: 30883786 DOI: 10.1111/nph.15800] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
The evolution of resistance to herbicides is a striking example of rapid, human-directed adaptation with major consequences for food production. Most studies of herbicide resistance are performed reactively and focus on post hoc determination of resistance mechanisms following the evolution of field resistance. If the evolution of resistance can be anticipated, however, pro-active management to slow or prevent resistance traits evolving can be advocated. We report a national-scale study that combines population monitoring, glyphosate sensitivity assays, quantitative genetics and epidemiological analyses to pro-actively identify the prerequisites for adaptive evolution (directional selection and heritable genetic variation) to the world's most widely used herbicide (glyphosate) in a major, economically damaging weed species, Alopecurus myosuroides. Results highlighted pronounced, heritable variability in glyphosate sensitivity amongst UK A. myosuroides populations. We demonstrated a direct epidemiological link between historical glyphosate selection and current population-level sensitivity, and show that current field populations respond to further glyphosate selection. This study provides a novel, pro-active assessment of adaptive potential for herbicide resistance, and provides compelling evidence of directional selection for glyphosate insensitivity in advance of reports of field resistance. The epidemiological approach developed can provide a basis for further pro-active study of resistance evolution across pesticide resistance disciplines.
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Affiliation(s)
- David Comont
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Helen Hicks
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, NG25 0QF, UK
| | - Laura Crook
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Richard Hull
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Elise Cocciantelli
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Jarrod Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Dylan Childs
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
| | - Robert Freckleton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
| | - Paul Neve
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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24
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Zhao N, Yan Y, Luo Y, Zou N, Liu W, Wang J. Unravelling mesosulfuron-methyl phytotoxicity and metabolism-based herbicide resistance in Alopecurus aequalis: Insight into regulatory mechanisms using proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:486-497. [PMID: 30904660 DOI: 10.1016/j.scitotenv.2019.03.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Non-target-site based resistance (NTSR), a poorly understood multigenic trait, has evolved as the greatest threat to crop production worldwide, by endowing weed plants an unpredictable pattern of resistance to herbicides. Our recent work with multiple-herbicide-resistant shortawn foxtail (Alopecurus aequalis Sobol.) biotype has preliminary indicated that cytochrome P450s-involved enhanced rate of mesosulfuron-methyl metabolism may involve in the NTSR. Here by further determining the differences in glutathione S-transferase (GST) activity and uptake and metabolic rates of mesosulfuron between resistant (R) and susceptible (S) A. aequalis plants, and associating them with endogenous differently regulated proteins (DEPs) identified from combinational proteomics analyses, we provided direct evidences on the enhanced herbicide degradation in resistant plants. Subsequently, the physiological phenotypes of photosynthesis, chlorophyll fluorescence, and antioxidation were compared between R and S plants and linked with correlative DEPs, indicating a series of key pathways including solar energy capture, photosynthetic electron transport, redox homeostasis, carbon fixation, photorespiration, and reactive oxygen species scavenging in susceptible plants were broken or severely damaged by mesosulfuron stress. In comparison, resistant plants have evolved enhanced herbicide degradation to minimize the accumulation of mesosulfuron and protect the photosynthesis and ascorbate-glutathione cycle against the adverse effects of chemical injury, giving A. aequalis plants a NTSR phenotype. Additionally, three key proteins respectively annotated as esterase, GST, and glucosyltransferase were identified and enabled as potential transcriptional markers for quick diagnosing the metabolic mesosulfuron resistance in A. aequalis species.
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Affiliation(s)
- Ning Zhao
- College of Plant Protection, Shandong Agricultural University, Tai'an, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yanyan Yan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yongli Luo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Nan Zou
- College of Plant Protection, Shandong Agricultural University, Tai'an, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an, China.
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25
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Comont D, Knight C, Crook L, Hull R, Beffa R, Neve P. Alterations in Life-History Associated With Non-target-site Herbicide Resistance in Alopecurus myosuroides. FRONTIERS IN PLANT SCIENCE 2019; 10:837. [PMID: 31297127 PMCID: PMC6607922 DOI: 10.3389/fpls.2019.00837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/12/2019] [Indexed: 05/22/2023]
Abstract
The evolution of resistance to herbicides is a classic example of rapid contemporary adaptation in the face of a novel environmental stress. Evolutionary theory predicts that selection for resistance will be accompanied by fitness trade-offs in environments where the stress is absent. Alopecurus myosuroides, an autumn-germinating grass weed of cereal crops in North-West Europe, has evolved resistance to seven herbicide modes-of-action, making this an ideal species to examine the presence and magnitudes of such fitness costs. Here, we use two contrasting A. myosuroides phenotypes derived from a common genetic background, one with enhanced metabolism resistance to a commercial formulation of the sulfonylurea (ALS) actives mesosulfuron and iodosulfuron, and the other with susceptibility to these actives (S). Comparisons of plant establishment, growth, and reproductive potential were made under conditions of intraspecific competition, interspecific competition with wheat, and over a gradient of nitrogen deprivation. Herbicide dose response assays confirmed that the two lines had contrasting resistance phenotypes, with a 20-fold difference in resistance between them. Pleiotropic effects of resistance were observed during plant development, with R plants having a greater intraspecific competitive effect and longer tiller lengths than S plants during vegetative growth, but with S plants allocating proportionally more biomass to reproductive tissues during flowering. Direct evidence of a reproductive cost of resistance was evident in the nitrogen deprivation experiment with R plants producing 27% fewer seed heads per plant, and a corresponding 23% reduction in total seed head length. However, these direct effects of resistance on fecundity were not consistent across experiments. Our results demonstrate that a resistance phenotype based on enhanced herbicide metabolism has pleiotropic impacts on plant growth, development and resource partitioning but does not support the hypothesis that resistance is associated with a consistent reproductive fitness cost in this species. Given the continued difficulties associated with unequivocally detecting costs of herbicide resistance, we advocate future studies that adopt classical evolutionary quantitative genetics approaches to determine genetic correlations between resistance and fitness-related plant life history traits.
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Affiliation(s)
- David Comont
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
- *Correspondence: David Comont,
| | - Craig Knight
- School of Life Sciences, University of Warwick, Wellesbourne, United Kingdom
| | - Laura Crook
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Richard Hull
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Roland Beffa
- Bayer AG, CropScience Division, Frankfurt, Germany
| | - Paul Neve
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
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