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Cusaro CM, Capelli E, Picco AM, Brusoni M. Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy. Sci Rep 2024; 14:10544. [PMID: 38719860 PMCID: PMC11078947 DOI: 10.1038/s41598-024-59856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
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.
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Affiliation(s)
- Carlo Maria Cusaro
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Enrica Capelli
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Anna Maria Picco
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Maura Brusoni
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy.
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Chen J, Cui H, Li Z, Yu H, Hou Q, Li X. Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate. Int J Mol Sci 2023; 24:ijms24098250. [PMID: 37175957 PMCID: PMC10179075 DOI: 10.3390/ijms24098250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Gene mutation is a basic evolutionary mechanism in plants under selection pressure of herbicides. Such mutation has pleiotropic effects on plant growth. We systemically investigated the effects of Pro106Leu (P106L), Pro106Ser (P106S), and Thr102Ile + Pro106Ser (TIPS) mutations on EPSPS functionality and fitness traits in Eleusine indica at the biochemical and physiological levels. The affinity of natural EPSPS for glyphosate was 53.8 times higher than that for phosphoenolpyruvate (PEP), as revealed by the dissociation constant; the constant decreased in both the P106L (39.9-fold) and P106S (46.9-fold) mutants but increased in the TIPS (87.5-fold) mutant. The Km (PEP) values of the P106L, P106S, and TIPS mutants were 2.4-, 0.7-, and 4.1-fold higher than that of natural EPSPS, corresponding to resistance levels of 2.5, 1.9, and 11.4, respectively. The catalytic efficiency values (maximum reaction rates) were 0.89-, 0.94-, and 0.26-fold higher than that of natural EPSPS. The levels of metabolites related to amino acids and nucleotides were significantly reduced in the mutated plants. The fitness costs were substantial for the biomass, total leaf area, seed number, and seedling emergence throughout the growth period in the plants with P106L and TIPS mutations. These results provide insights into EPSPS kinetics and their effect on plant growth.
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Affiliation(s)
- Jingchao Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hailan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiling Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haiyan Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiang Hou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangju Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Chen R, Wang S, Sun Y, Li H, Wan S, Lin F, Xu H. Comparison of Glyphosate-Degradation Ability of Aldo-Keto Reductase (AKR4) Proteins in Maize, Soybean and Rice. Int J Mol Sci 2023; 24:ijms24043421. [PMID: 36834831 PMCID: PMC9966811 DOI: 10.3390/ijms24043421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Genes that participate in the degradation or isolation of glyphosate in plants are promising, for they endow crops with herbicide tolerance with a low glyphosate residue. Recently, the aldo-keto reductase (AKR4) gene in Echinochloa colona (EcAKR4) was identified as a naturally evolved glyphosate-metabolism enzyme. Here, we compared the glyphosate-degradation ability of theAKR4 proteins from maize, soybean and rice, which belong to a clade containing EcAKR4 in the phylogenetic tree, by incubation of glyphosate with AKR proteins both in vivo and in vitro. The results indicated that, except for OsALR1, the other proteins were characterized as glyphosate-metabolism enzymes, with ZmAKR4 ranked the highest activity, and OsAKR4-1 and OsAKR4-2 exhibiting the highest activity among the AKR4 family in rice. Moreover, OsAKR4-1 was confirmed to endow glyphosate-tolerance at the plant level. Our study provides information on the mechanism underlying the glyphosate-degradation ability of AKR proteins in crops, which enables the development of glyphosate-resistant crops with a low glyphosate residue, mediated by AKRs.
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Affiliation(s)
| | | | | | | | | | - Fei Lin
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
| | - Hanhong Xu
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
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Brunharo CACG, Streisfeld MA. Multiple evolutionary origins of glyphosate resistance in
Lolium multiflorum. Evol Appl 2022; 15:316-329. [PMID: 35233250 PMCID: PMC8867705 DOI: 10.1111/eva.13344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 11/29/2022] Open
Abstract
The multitude of herbicide resistance patterns that have evolved in different weed species is a remarkable example of the rapid adaptation to anthropogenic‐driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of Lolium multiflorum in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine whether known mechanisms were responsible for glyphosate resistance and whether resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance. We found no evidence of genetic alterations or expression changes at known target and non‐target‐site resistance mechanisms of glyphosate. Population genomic analyses indicated that resistant populations tended to have largely distinct ancestry from one another, suggesting that glyphosate resistance did not spread among populations by gene flow. Rather, resistance appears to have evolved independently on different genetic backgrounds. We also detected potential loci associated with the resistance phenotype, some of which encode proteins with potential effects on herbicide metabolism. Our results suggest that Oregon populations of L. multiflorum evolved resistance to glyphosate due to a novel mechanism. Future studies that characterize the gene or genes involved in resistance will be necessary to confirm this conclusion.
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Vázquez-García JG, Rojano-Delgado AM, Alcántara-de la Cruz R, Torra J, Dellaferrera I, Portugal J, De Prado R. Distribution of Glyphosate-Resistance in Echinochloa crus-galli Across Agriculture Areas in the Iberian Peninsula. FRONTIERS IN PLANT SCIENCE 2021; 12:617040. [PMID: 33679831 PMCID: PMC7928338 DOI: 10.3389/fpls.2021.617040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
The levels of resistance to glyphosate of 13 barnyard grass (Echinochloa crus-galli) populations harvested across different agriculture areas in the Southern Iberian Peninsula were determined in greenhouse and laboratory experiments. Shikimate accumulation fast screening separated the populations regarding resistance to glyphosate: susceptible (S) E2, E3, E4, and E6 and resistant (R) E1, E5, E7, E8, E9, E10, E11, E12, and E13. However, resistance factor (GR50 E1-E13/GR50 E6) values separated these populations into three groups: (S) E2, E3, E4, and E6, (R) E1, E5, E7, E8, and E9, and very resistant (VR) E10, E11, E12, and E13. 14C-glyphosate assays performed on two S populations (E2 and E6) showed greater absorption and translocation than those found for R (E7 and E9) and VR (E10 and E12) populations. No previous population metabolized glyphosate to amino methyl phosphonic acid (AMPA) and glyoxylate, except for the E10 population that metabolized 51% to non-toxic products. The VR populations showed two times more 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity without herbicide than the rest, while the inhibition of the EPSPS activity by 50% (I50) required much higher glyphosate in R and VR populations than in S populations. These results indicated that different target-site and non-target-site resistance mechanisms were implicated in the resistance to glyphosate in E. crus-galli. Our results conclude that resistance is independent of climate, type of crop, and geographic region and that the level of glyphosate resistance was mainly due to the selection pressure made by the herbicide on the different populations of E. crus-galli studied.
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Affiliation(s)
- José G. Vázquez-García
- Department of Agricultural Chemistry and Edaphology, University of Córdoba, Córdoba, Spain
| | | | | | - Joel Torra
- Department d’Hortofruticultura, Botànica i Jardineria, Agrotecnio, Universitat de Lleida, Lleida, Spain
| | - Ignacio Dellaferrera
- Faculty of Agricultural Sciences, National University of the Litoral, Esperanza, Argentina
- National Scientific and Technical Research Council, Godoy Cruz, Argentina
| | - João Portugal
- Biosciences Department, Polytechnic Institute of Beja, Beja, Portugal
- VALORIZA-Research Centre for Endogenous Resource Valorization, Polytechnic Institute of Portalegre, Portalegre, Portugal
| | - Rafael De Prado
- Department of Agricultural Chemistry and Edaphology, University of Córdoba, Córdoba, Spain
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Baek Y, Bobadilla LK, Giacomini DA, Montgomery JS, Murphy BP, Tranel PJ. Evolution of Glyphosate-Resistant Weeds. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 255:93-128. [PMID: 33932185 DOI: 10.1007/398_2020_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.
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Affiliation(s)
- Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | | - Brent P Murphy
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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Fang J, Zhang Y, Liu T, Yan B, Li J, Dong L. Target-Site and Metabolic Resistance Mechanisms to Penoxsulam in Barnyardgrass ( Echinochloa crus-galli (L.) P. Beauv). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8085-8095. [PMID: 31265279 DOI: 10.1021/acs.jafc.9b01641] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Herbicide resistance identification is essential for effective chemical weed control. In this study, we quantified the differences in growth response between penoxsulam resistant (R) and sensitive (S) Echinochloa crus-galli populations, explored the changes in ALS, and performed genetic analyses to identify metabolic genes that are up-regulated by the application of penoxsulam and other common herbicides. The R population showed a 26.0-fold higher resistance to penoxsulam and varied resistance to most tested herbicides with indices ranging from 4.9 to 145.9. A Trp-574-Arg amino acid mutation in ALS and low penoxsulam ALS sensitivity were the main mechanisms underlying herbicide resistance. The penoxsulam resistance can be significantly reversed by two P450s inhibitors and one GST inhibitor. By RNA-Seq, thirty-six highly expressed contigs were selected, and 30 of them were up-regulated in the R population treated by penoxsulam. Many of these genes were significantly expressed when treated with pyroxsulam, metamifop, and quinclorac. These upregulated genes appear to be complementary for plant resistance to penoxsulam and other common herbicides.
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Affiliation(s)
- Jiapeng Fang
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Yuhua Zhang
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Tingting Liu
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Bojun Yan
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Jun Li
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Liyao Dong
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
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8
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Vila-Aiub MM, Yu Q, Powles SB. Do plants pay a fitness cost to be resistant to glyphosate? THE NEW PHYTOLOGIST 2019; 223:532-547. [PMID: 30737790 DOI: 10.1111/nph.15733] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
We reviewed the literature to understand the effects of glyphosate resistance on plant fitness at the molecular, biochemical and physiological levels. A number of correlations between enzyme characteristics and glyphosate resistance imply the existence of a plant fitness cost associated with resistance-conferring mutations in the glyphosate target enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). These biochemical changes result in a tradeoff between the glyphosate resistance of the EPSPS enzyme and its catalytic activity. Mutations that endow the highest resistance are more likely to decrease catalytic activity by reducing the affinity of EPSPS for its natural substrate, and/or slowing the velocity of the enzyme reaction, and are thus very likely to endow a substantial plant fitness cost. Prediction of fitness costs associated with EPSPS gene amplification and overexpression can be more problematic. The validity of cost prediction based on the theory of evolution of gene expression and resource allocation has been cast into doubt by contradictory experimental evidence. Further research providing insights into the role of the EPSPS cassette in weed adaptation, and estimations of the energy budget involved in EPSPS amplification and overexpression are required to understand and predict the biochemical and physiological bases of the fitness cost of glyphosate resistance.
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Affiliation(s)
- Martin M Vila-Aiub
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
- IFEVA - CONICET - Faculty of Agronomy, Department of Ecology, University of Buenos Aires (UBA), Buenos Aires, 1417, Argentina
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
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Brunharo CADCG, Morran S, Martin K, Moretti ML, Hanson BD. EPSPS duplication and mutation involved in glyphosate resistance in the allotetraploid weed species Poa annua L. PEST MANAGEMENT SCIENCE 2019; 75:1663-1670. [PMID: 30506940 DOI: 10.1002/ps.5284] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Poa annua is a widespread winter annual weed species in California. Recently, poor control of this species with glyphosate was reported by growers in an almond orchard in California with a history of repetitive glyphosate use. The objectives of this research were to evaluate the level of glyphosate resistance in a developed S4 P. annua line (R) and identify the mechanisms of resistance involved. RESULTS Whole-plant dose-response experiments confirmed glyphosate resistance in R, which required 18-fold more glyphosate to achieve a 50% growth reduction compared with a susceptible line (S), results that were supported by the lower shikimate accumulation observed in R compared with S. No differences in glyphosate absorption, translocation, or metabolism were observed, suggesting that non-target-site mechanisms of resistance are not involved in the resistance phenotype. A missense single nucleotide polymorphism was observed in EPSPS coding position 106 in R, resulting in a leucine to proline substitution. This polymorphism was observed exclusively in P. supina EPSPS homeologs. A seven-fold increase in the number of copies of EPSPS alleles was observed in R compared with S. CONCLUSIONS We report the first case of glyphosate resistance associated with both EPSPS duplication and target-site mutation at position 106, leading to high levels of glyphosate resistance in the allotetraploid weed species Poa annua L. Data obtained in this research will be useful for the development of diagnostic tools for rapid glyphosate resistance identification, monitoring and containment. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | - Sarah Morran
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Katie Martin
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Marcelo L Moretti
- Department of Horticulture, Oregon State University, Corvallis, OR, USA
| | - Bradley D Hanson
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
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