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Pagnoncelli Jr FDB, Losada FB, Alvear MJG, Gonzalez-Andujar JL, Trezzi MM, Bittencourt HVH, Salomão HM. Response characterization and target site mechanism study in glyphosate-resistant populations of Lolium multiflorum L. from Brazil. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 198:105737. [PMID: 38225083 DOI: 10.1016/j.pestbp.2023.105737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Italian ryegrass (Lolium multiflorum L.) is an invasive species widely spread in croplands worldwide. The intensive use of glyphosate has resulted in the selection of resistance to this herbicide in Italian ryegrass. This work characterized the response to glyphosate of Italian ryegrass populations from the South and Southwest regions of Paraná, Brazil. A total of 44 Italian ryegrass populations were collected in farming areas, and were classified for glyphosate resistance with 75% of populations resistant to gloyphosate. Of these, 3 resistant (VT05AR, MR20AR and RN01AR) and three susceptible (VT07AS, MR05AS and RN01AS) of these populations were selected to determine the resistance level and the involvement of the target site mechanisms for glyphosate resistance. Susceptible populations GR50 ranged from 165.66 to 218.17 g.e.a. ha-1 and resistant populations from 569.37 to 925.94, providing RI ranging from 2.88 and 4.70. No mutation in EPSPS was observed in the populations, however, in two (MR20AR and RN02AR) of the three resistant populations, an increase in the number of copies of the EPSPs gene (11 to 57×) was detected. The number of copies showed a positive correlation with the gene expression (R2 = 0.86) and with the GR50 of the populations (R2 = 0.81). The increase in EPSPS gene copies contributes to glyphosate resistance in Italian ryegrass populations from Brazil.
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Affiliation(s)
| | - Francisco Barro Losada
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo, 14004 Cordoba, Spain
| | - Maria Jose Gimenez Alvear
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo, 14004 Cordoba, Spain
| | - Jose L Gonzalez-Andujar
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Spain and International Laboratory on Global Change (LINCGlobal) (CSIC), Alameda del Obispo, 14005 Cordoba, Spain
| | - Michelangelo Muzell Trezzi
- Department of Agricultural Sciences, Federal Technological University of Paraná, Via do Conhecimento, km 01, 85503-390 Pato Branco, Paraná, Brazil.
| | - Henrique Von Hertwig Bittencourt
- Department of Agronomy, Federal University of Fronteira Sul, BR-158, s/n, Zona Rural, 85301-970-Laranjeiras do Sul, Paraná, Brazil
| | - Helis Marina Salomão
- Department of Agricultural Sciences, Federal Technological University of Paraná, Via do Conhecimento, km 01, 85503-390 Pato Branco, Paraná, Brazil
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Schwedt I, Schöne K, Eckert M, Pizzinato M, Winkler L, Knotkova B, Richts B, Hau JL, Steuber J, Mireles R, Noda-Garcia L, Fritz G, Mittelstädt C, Hertel R, Commichau FM. The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates. Environ Microbiol 2023; 25:3604-3622. [PMID: 37822042 DOI: 10.1111/1462-2920.16518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023]
Abstract
Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.
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Affiliation(s)
- Inge Schwedt
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Kerstin Schöne
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Maike Eckert
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Manon Pizzinato
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Winkler
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Barbora Knotkova
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University of Göttingen, Göttingen, Germany
| | - Björn Richts
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University of Göttingen, Göttingen, Germany
| | - Jann-Louis Hau
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Julia Steuber
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Raul Mireles
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
| | - Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
| | - Günter Fritz
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Carolin Mittelstädt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
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3
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Wang R, Sun Y, Lan Y, Wei S, Huang H, Li X, Huang Z. ALS gene overexpression and enhanced metabolism conferring Digitaria sanguinalis resistance to nicosulfuron in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1290600. [PMID: 38046608 PMCID: PMC10690955 DOI: 10.3389/fpls.2023.1290600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023]
Abstract
Crabgrass (Digitaria sanguinalis) is a common malignant weed in corn fields in China. Recently, the acetolactate synthase (ALS) inhibitor, nicosulfuron, has shown decreasing efficacy against crabgrass. In order to elucidate the molecular basis of resistance to nicosulfuron in crabgrass, we conducted bioassays, combined with gene sequence analysis, relative expression and relative copy number analysis, to characterize resistance in crabgrass populations collected from Beijing, Heilongjiang, Jilin and Anhui provinces. Whole-plant dose-response results indicated that only population collected in Heilongjiang province (HLJ) had developed low level of resistance to nicosulfuron compared with the sensitive population (SD22). No known resistant mutation of ALS gene was found in HLJ population. The real-time fluorescence quantitative PCR results showed that the ALS gene copy number did not differ significantly between the HLJ and SD22 populations. However, the ALS gene expression in the HLJ was 2.07-fold higher than that of the SD22 population at 24 h after treatment with nicosulfuron. Pretreatment with the cytochrome P450 (CYP450) inhibitor malathion, piperonyl butoxide (PBO), and the glutathione S-transferase (GST) inhibitor 4-Chloro-7-nitro-1,2,3-benzoxadiazole (NBD-Cl) all partially reversed HLJ resistance. Among them, the synergistic effect of PBO and nicosulfuron is the most significant. This is the first report of resistance to nicosulfuron in crabgrass through ALS gene overexpression and possible metabolic resistance.
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Affiliation(s)
- Ruolin Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Plant Protection, Northeast Agricultural University, Harbin, China
| | - Yuning Lan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shouhui Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjuan Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangju Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaofeng Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Yamada T, Maeda M, Nagai H, Salamin K, Chang YT, Guenova E, Feuermann M, Monod M. Two different types of tandem sequences mediate the overexpression of TinCYP51B in azole-resistant Trichophyton indotineae. Antimicrob Agents Chemother 2023; 67:e0093323. [PMID: 37823662 PMCID: PMC10648874 DOI: 10.1128/aac.00933-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/03/2023] [Indexed: 10/13/2023] Open
Abstract
Trichophyton indotineae is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant T. indotineae-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding TinCYP51B in tandem specifically at the CYP51B locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring TinCYP51B. Consequently, two types of T. indotineae azole-resistant strains were found to host TinCYP51B in tandem sequences (type I with 2,404 bp TinCYP51B blocks and type II with 7,374 bp TinCYP51B blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of TinCYP51B within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without TinCYP51B duplication, showing that azole resistance in T. indotineae strains is mediated by one of two types of TinCYP51B amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.
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Affiliation(s)
- Tsuyoshi Yamada
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
- Asia International Institute of Infectious Disease Control, Teikyo University, Tokyo, Japan
| | - Mari Maeda
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | | | - Karine Salamin
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Yun-Tsan Chang
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Emmanuella Guenova
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Marc Feuermann
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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Koo DH, Ju Y, Putta K, Sathishraj R, Roma-Burgos N, Jugulam M, Friebe B, Gill BS. Extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. PEST MANAGEMENT SCIENCE 2023; 79:4290-4294. [PMID: 37345512 DOI: 10.1002/ps.7626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND An Italian ryegrass population from Arkansas, USA developed glyphosate resistance due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. The plants in this population with approximately 70 EPSPS copies were used in the present study for the physical mapping of amplified copies of EPSPS gene to determine the possible mechanism of EPSPS gene amplification conferring glyphosate resistance in Italian ryegrass. RESULT Fluorescence in situ hybridization (FISH) analysis of glyphosate resistant (GR) Italian ryegrass plants with approximately 70 EPSPS copies displayed EPSPS hybridization signals randomly on most of the metaphase chromosomes. Glyphosate susceptible (GS) Italian ryegrass plants with one EPSPS copy displayed single prominent EPSPS hybridization signal, which was co-localized with 5S rDNA locus along with few additional signals on the outside of chromosomes. Pulsed-field gel electrophoresis (PFGE) followed by DNA blot using EPSPS gene as a probe identified a prominent EPSPS hybridization around the 400 kb region in GR DNA samples, but not in GS DNA samples. CONCLUSION We report the extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. Physical mapping of amplified copies of EPSPS gene in Italian ryegrass by FISH gives us a clue that the amplified copies of EPSPS gene may be present in the extrachromosomal DNA elements. Further analysis by PFGE followed by DNA blotting revealed that the extrachromosomal DNA containing EPSPS is approximately 400 kb similar in size with that of eccDNA replicon in Amaranthus palmeri. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yoonha Ju
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Rajendran Sathishraj
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Nilda Roma-Burgos
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
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Koo DH, Sathishraj R, Nakka S, Ju Y, Nandula VK, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-mediated spread of herbicide resistance in interspecific hybrids of pigweed. PLANT PHYSIOLOGY 2023; 193:229-233. [PMID: 37186777 PMCID: PMC10469533 DOI: 10.1093/plphys/kiad281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are found in many eukaryotic organisms. EccDNA-powered copy number variation plays diverse roles, from oncogenesis in humans to herbicide resistance in crop weeds. Here, we report interspecific eccDNA flow and its dynamic behavior in soma cells of natural populations and F1 hybrids of Amaranthus sp. The glyphosate-resistance (GR) trait is controlled by eccDNA-based amplification harboring the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (eccDNA replicon), the molecular target of glyphosate. We documented pollen-mediated transfer of eccDNA in experimental hybrids between glyphosate-susceptible Amaranthus tuberculatus and GR Amaranthus palmeri. Experimental hybridization and fluorescence in situ hybridization (FISH) analysis revealed that the eccDNA replicon in Amaranthus spinosus derived from GR A. palmeri by natural hybridization. FISH analysis also revealed random chromosome anchoring and massive eccDNA replicon copy number variation in soma cells of weedy hybrids. The results suggest that eccDNAs are inheritable across compatible species, contributing to genome plasticity and rapid adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Sridevi Nakka
- Heartland Plant Innovations Inc., Manhattan, KS 66506, USA
| | - Yoonha Ju
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Vijay K Nandula
- National Institute of Food and Agriculture, USDA, Kansas City, MO 64105, USA
- Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS 38776, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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Yanniccari M, Palma-Bautista C, Vázquez-García JG, Gigón R, Mallory-Smith CA, De Prado R. Constitutive overexpression of EPSPS by gene duplication is involved in glyphosate resistance in Salsola tragus. PEST MANAGEMENT SCIENCE 2023; 79:1062-1068. [PMID: 36327342 DOI: 10.1002/ps.7272] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Glyphosate-resistant Salsola tragus accessions have been identified in the USA and Argentina; however, the mechanisms of glyphosate resistance have not been elucidated. The goal of this study was to determine the mechanism/s of glyphosate resistance involved in two S. tragus populations (R1 and R2) from Argentina. RESULTS Both glyphosate-resistant populations had a six-fold lower sensitivity to glyphosate than the S population (i.e. resistance index). No evidence of differential absorption, translocation or metabolism of glyphosate was found in the R1 and R2 populations compared to a susceptible population (S). No 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) mutations were detected, but S. tragus R1 and R2 plants had ≈14-fold higher EPSPS gene relative copy number compared to the S counterpart. In R1 and R2, EPSPS duplication entailed a greater constitutive EPSPS transcript abundance by approximately seven-fold and a basal EPSPS activity approximately three-fold higher than the S population. CONCLUSION The current study reports EPSPS gene duplication for the first time as a mechanism of glyphosate resistance in S. tragus populations. The increase of glyphosate dose needed to kill R1 and R2 plants was linked to the EPSPS transcript abundance and level of EPSPS activity. This evidence supports the convergent evolution of the overexpression of the EPSPS gene in several Chenopodiaceae/Amaranthaceae species adapted to drought environments and the role of gene duplication as an adaptive advantage for plants to withstand stress. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Marcos Yanniccari
- Chacra Experimental Integrada Barrow (MDA-INTA), National Scientific and Technical Research Council (CONICET), Faculty of Agronomy, National University of La Pampa, La Pampa, Argentina
| | - Candelario Palma-Bautista
- Department of Agroforestry, Plant Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
| | | | - Ramón Gigón
- Private Consultant in Weed Control, Tres Arroyos, Argentina
| | | | - Rafael De Prado
- Department of Agroforestry, Plant Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
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Molina-Santiago C, Udaondo Z. Mechanisms of resistance to glyphosate: an example of bacterial adaptability to anthropogenic substances. Environ Microbiol 2022; 24:3313-3315. [PMID: 35355369 DOI: 10.1111/1462-2920.15989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205
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Yang J, Jiang M, Jia S, Liao M, Cao H, Zhao N. Expression Pattern of Entire Cytochrome P450 Genes and Response of Defenses in a Metabolic-Herbicide-Resistant Biotype of Polypogon fugax. FRONTIERS IN PLANT SCIENCE 2022; 13:868807. [PMID: 35401603 PMCID: PMC8990753 DOI: 10.3389/fpls.2022.868807] [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: 02/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Enhanced herbicide metabolism mediated by cytochrome P450s has been proposed as one of the major mechanisms of resistance to fenoxaprop-P-ethyl in a metabolic-herbicide-resistant biotype of Asia minor bluegrass (Polypogon fugax Nees ex Steud.). Upon pre-treatment with the P450 inhibitor piperonyl butoxide, a remarkable reduction in metabolic rates of the phytotoxic fenoxaprop-P has been observed in the resistant plants, implying that constitutive and/or fenoxaprop-P-ethyl-induced up-regulation of specific P450 isoforms are involved in the fenoxaprop-P-ethyl resistance. However, which P450 gene(s) were responsible for the metabolic resistance is still unknown. In this present study, based on the abundant gene resources of P. fugax established previously, a total of 48 putative P450 genes were isolated from the metabolic-herbicide-resistant plants and used for gene expression analysis. The most suitable reference genes for accurate normalization of real-time quantitative PCR data were first identified in P. fugax and recognized as actin (ACT), 18S rRNA (18S), and ribulose-1,5-bisphosphate carboxylase oxygenase (RUBP) under fenoxaprop-P-ethyl stress, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and elongation factor 1α (EF1α) under mesosulfuron-methyl stress, and ACT, EF1α, eukaryotic initiation factor 4a (EIF4A), and 25S rRNA (25S) at different growth stages. Expression analysis of the putative P450 genes revealed that six genes, respectively, annotated as CYP709B1, CYP71A1-4, CYP711A1, CYP78A9, P450-11, and P450-39 were up-regulated more than 10-fold in the resistant plants by fenoxaprop-P-ethyl treatment, and all of them exhibited constitutively and/or herbicide-induced higher transcript levels in the fenoxaprop-P-ethyl-resistant than in the susceptible plants. Three genes, respectively, annotated as CYPRO4, CYP313A4, and CYP51H11 constantly up-regulated in the resistant than in the susceptible plants after fenoxaprop-P-ethyl treatment. Up-regulated expressions of these specific P450 genes were consistent with the higher P450 contents determined in the resistant plants. These results will help to elucidate the mechanisms for P450-mediated metabolic-herbicide resistance in P. fugax as well as other grass weed species.
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Affiliation(s)
- Jiajia Yang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Minghao Jiang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Siwei Jia
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Ning Zhao
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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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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Koo DH, Sathishraj R, Friebe B, Gill BS. Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics. Cytogenet Genome Res 2022; 161:578-584. [PMID: 35021177 DOI: 10.1159/000521409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
In agriculture, various chemicals are used to control the weeds. Out of which, glyphosate is an important herbicide invariably used in the cultivation of glyphosate-resistant crops to control weeds. Overuse of glyphosate results in the evolution of glyphosate-resistant weeds. Evolution of glyphosate resistance (GR) in Amaranthus palmeri (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to >160-fold increase in copies of the EPSPS gene than in a glyphosate-susceptible (GS) population. This increased copy number of the EPSPS gene increased the genome size ranging from 3.5 to 11.8%, depending on the copy number compared to the genome size of GS AP. FISH analysis using a 399-kb EPSPS cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified EPSPS copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The EPSPS gene-containing eccDNA having a size of ∼400 kb is termed EPSPS-eccDNA and showed somatic mosacism in size and copy number. EPSPS-eccDNA has a genetic mechanism to tether randomly to mitotic or meiotic chromosomes during cell division or gamete formation and is inherited to daughter cells or progeny generating copy number variation. These eccDNAs are stable genetic elements that can replicate and exist independently. The genomic characterization of the EPSPS locus, along with the flanking regions, identified the presence of a complex array of repeats and mobile genetic elements. The cytogenomics approach in understanding the biology of EPSPS-eccDNA sheds light on various characteristics of EPSPS-eccDNA that favor GR in AP.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
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12
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Heckel DG. Perspectives on gene copy number variation and pesticide resistance. PEST MANAGEMENT SCIENCE 2022; 78:12-18. [PMID: 34480789 DOI: 10.1002/ps.6631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/28/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Although the generation of evolutionary diversity by gene duplication has long been known, the implications for pesticide resistance are just now beginning to be appreciated. A few examples will be cited to illustrate the point that there are many variations on the theme that gene duplication does not follow a set pattern. Transposable elements may facilitate the process but the mechanistic details are obscure and unpredictable. New developments in DNA sequencing technology and genome assembly promise to reveal more examples, yet care must be taken in interpreting the results of transcriptome and genome assemblies and independent means of validation are important. Once a specific gene family is identified, special methods generally must be used to avoid underestimating population polymorphisms and being trapped in preconceptions about the simplicity of the process. © 2021 The Author. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- David G Heckel
- Max Planck Institute for Chemical Ecology, Jena, Germany
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13
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Adu-Yeboah P, Malone JM, Gill G, Preston C. Non-Mendelian inheritance of gene amplification-based resistance to glyphosate in Hordeum glaucum (barley grass) from South Australia. PEST MANAGEMENT SCIENCE 2021; 77:4298-4302. [PMID: 34148281 DOI: 10.1002/ps.6518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/19/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Hordeum glaucum Steud. is an important grass weed species in South Australia that has evolved resistance to glyphosate. This study investigated the mode of inheritance of glyphosate resistance in this species. RESULTS Hand-pollination of glyphosate susceptible and resistant populations generated two F1 individuals, selfed to yield F2 progenies. In dose-response experiments, the F2 progenies showed intermediate response between the two parent populations. High variation in EPSPS gene copies was observed among F2 individuals, with some individuals possessing more gene copies than the resistant parent population. No evidence of a Mendelian single-gene pattern of inheritance was observed. CONCLUSION Inheritance of gene amplification in H. glaucum is non-Mendelian. © 2021 Society of Chemical Industry.
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Affiliation(s)
| | - Jenna M Malone
- School of Agriculture, University of Adelaide, Glen Osmond, Australia
| | - Gurjeet Gill
- School of Agriculture, University of Adelaide, Glen Osmond, Australia
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14
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Cockerton HM, Kaundun SS, Nguyen L, Hutchings SJ, Dale RP, Howell A, Neve P. Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population. FRONTIERS IN PLANT SCIENCE 2021; 12:651381. [PMID: 34267768 PMCID: PMC8276266 DOI: 10.3389/fpls.2021.651381] [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: 01/09/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. The growth and fitness of seed families with contrasting levels of glyphosate resistance was assessed in the absence of glyphosate to determine their ability to compete for resources under intra- and interspecific competition. We identified a positive correlation between the level of glyphosate resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus identifying gene amplification as the mechanism of resistance within the population. Resistant A. tuberculatus plants were found to have a lower competitive response when compared to the susceptible phenotypes with 2.76 glyphosate resistant plants being required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.
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Affiliation(s)
- Helen M. Cockerton
- NIAB EMR, Kent, United Kingdom
- Warwick Crop Centre, The University of Warwick Wellesbourne, Warwick, United Kingdom
| | - Shiv S. Kaundun
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | | | - Sarah Jane Hutchings
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Richard P. Dale
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Anushka Howell
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Paul Neve
- Warwick Crop Centre, The University of Warwick Wellesbourne, Warwick, United Kingdom
- Rothamsted Research, Harpenden, United Kingdom
- Department of Plant and Environmental Sciences, University of Copenhagen, Tåstrup, Denmark
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15
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Hertel R, Gibhardt J, Martienssen M, Kuhn R, Commichau FM. Molecular mechanisms underlying glyphosate resistance in bacteria. Environ Microbiol 2021; 23:2891-2905. [PMID: 33876549 DOI: 10.1111/1462-2920.15534] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/29/2022]
Abstract
Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.
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Affiliation(s)
- Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Marion Martienssen
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Ramona Kuhn
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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16
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Borges MPDS, Silva DV, Souza MDF, Silva TS, Teófilo TMDS, da Silva CC, Pavão QS, Passos ABRDJ, Dos Santos JB. Glyphosate effects on tree species natives from Cerrado and Caatinga Brazilian biome: Assessing sensitivity to two ways of contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144113. [PMID: 33486169 DOI: 10.1016/j.scitotenv.2020.144113] [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: 10/02/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Glyphosate is applied for dissection in no-till and post-emergence management in transgenic crops in agricultural fields near the Cerrado and Caatinga biomes. These biomes together represent 33.8% of the Brazilian territory, contributing to the maintenance of great world diversity in flora and fauna. Despite actions to protect them, the proximity with agricultural areas and intense use of glyphosate puts at risk the preservation of native vegetation due to the contamination via herbicide transport processes. Our objectives were: i) to determine the sensitivity of native species from the Cerrado and Caatinga to glyphosate contamination via drift and groundwater; ii) evaluate the level of sensitivity to glyphosate among the different organs of plants. The highest intoxications (upper 80%) were observed for Bauhinia cheilantha, Mimosa caesalpiniaefolia, Mimosa tenuiflora and Amburana cearensis due to drift simullation. The species with 90% of total dry matter reduction were Bauhinia cheilantha, Enterolobium contortisiliquum, Mimosa caesalpiniaefolia, Mimosa tenuiflora, Tabebuia aurea. B. cheilantha and M. tenuiflora are most affected by exposure to glyphosate drift, with 50% of total dry matter reduction when exposed to doses below 444,0 g ha-1. Leaf growth is more sensitive to glyphosate for drift exposure for most species. Hymenaea courbaril is an exception, with greater sensitivity to root growth (50% dry matter reduction at doses below 666,0 g ha-1). B. cheilantha is the species most sensitive to drift exposure; however, it showed complete tolerance to contamination in subsurface waters. Other species such as Anadenanthera macrocarpa and M. caesalpiniifolia are also sensitive to drift, but without reach 90% of total dry matter reduction. A. macrocarpa, M. caesalpiniifolia and T. aurea were tolerant to contamination by subsurface water. The differential tolerance of trees confirms glyphosate's potential as a species selection agent in the Cerrado and Caatinga biomes.
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Affiliation(s)
- Maiara Pinheiro da Silva Borges
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil.
| | - Daniel Valadão Silva
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Matheus de Freitas Souza
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Tatiane Severo Silva
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Taliane Maria da Silva Teófilo
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Cydianne Cavalcante da Silva
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Quésia Sá Pavão
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - Ana Beatriz Rocha de Jesus Passos
- Universidade Federal Rural do Semi-Árido, Agricultural Science Center, Av. Francisco Mota, 572, Costa e Silva, CEP 59625-900 Mossoró, RN, Brazil
| | - José Barbosa Dos Santos
- Universidade Federal dos Vales do Jequitinhonha e Mucuri - Campus JK, Agricultural Science Center, Rodovia MGT 367, Km 583, n° 5000, Alto da Jacuba, CEP: 39100-000 Diamantina, MG, Brazil
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17
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Tranel PJ. Herbicide resistance in Amaranthus tuberculatus †. PEST MANAGEMENT SCIENCE 2021; 77:43-54. [PMID: 32815250 DOI: 10.1002/ps.6048] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 05/23/2023]
Abstract
Amaranthus tuberculatus is the major weed species in many midwestern US row-crop production fields, and it is among the most problematic weeds in the world in terms of its ability to evolve herbicide resistance. It has now evolved resistance to herbicides spanning seven unique sites of action, with populations and even individual plants often possessing resistance to several herbicides/herbicide groups. Historically, herbicide target-site changes accounted for most of the known resistance mechanisms in this weed; however, over the last few years, non-target-site mechanisms, particularly enhanced herbicide detoxification, have become extremely common in A. tuberculatus. Unravelling the genetics and molecular details of non-target-site resistance mechanisms, understanding the extent to which they confer cross resistance to other herbicides, and understanding how they evolve remain as critical research endeavors. Transcriptomic and genomics approaches are already facilitating such studies, the results of which hopefully will inform better resistance-mitigation strategies. The largely unprecedented level of herbicide resistance in A. tuberculatus is not only a fascinating example of evolution in action, but it is a serious and growing threat to the sustainability of midwestern US cropping systems. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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18
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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: 9] [Impact Index Per Article: 3.0] [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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19
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Ali HBM, Osman SA. Ribosomal DNA localization on Lathyrus species chromosomes by FISH. J Genet Eng Biotechnol 2020; 18:63. [PMID: 33079306 PMCID: PMC7575666 DOI: 10.1186/s43141-020-00075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Fluorescence In Situ Hybridization (FISH) played an essential role to locate the ribosomal RNA genes on the chromosomes that offered a new tool to study the chromosome structure and evolution in plant. The 45S and 5S rRNA genes are independent and localized at one or more loci per the chromosome complement, their positions along chromosomes offer useful markers for chromosome discriminations. In the current study FISH has been performed to locate 45S and 5S rRNA genes on the chromosomes of nine Lathyrus species belong to five different sections, all have chromosome number 2n=14, Lathyrus gorgoni Parl, Lathyrus hirsutus L., Lathyrus amphicarpos L., Lathyrus odoratus L., Lathyrus sphaericus Retz, Lathyrus incospicuus L, Lathyrus paranensis Burkart, Lathyrus nissolia L., and Lathyrus articulates L. RESULTS The revealed loci of 45S and 5S rDNA by FISH on metaphase chromosomes of the examined species were as follow: all of the studied species have one 45S rDNA locus and one 5S rDNA locus except L. odoratus L., L. amphicarpos L. and L. sphaericus Retz L. have two loci of 5S rDNA. Three out of the nine examined species have the loci of 45S and 5S rRNA genes on the opposite arms of the same chromosome (L. nissolia L., L. amphicarpos L., and L. incospicuus L.), while L. hirsutus L. has both loci on the same chromosome arm. The other five species showed the loci of the two types of rDNA on different chromosomes. CONCLUSION The detected 5S and 45S rDNA loci in Lathyrus could be used as chromosomal markers to discriminate the chromosome pairs of the examined species. FISH could discriminate only one chromosome pair out of the seven pairs in three species, in L. hirsutus L., L. nissolia L. and L. incospicuus L., and two chromosome pairs in five species, in L. paranensis Burkart, L. odoratus L., L. amphicarpos L., L. gorgoni Parl. and L. articulatus L., while it could discriminate three chromosome pairs in L. sphaericus Retz. these results could contribute into the physical genome mapping of Lathyrus species and the evolution of rDNA patterns by FISH in the coming studies in future.
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Affiliation(s)
- Hoda B. M. Ali
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, P.O. 12622 Egypt
| | - Samira A. Osman
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, P.O. 12622 Egypt
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20
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Zulet-González A, Barco-Antoñanzas M, Gil-Monreal M, Royuela M, Zabalza A. Increased Glyphosate-Induced Gene Expression in the Shikimate Pathway Is Abolished in the Presence of Aromatic Amino Acids and Mimicked by Shikimate. FRONTIERS IN PLANT SCIENCE 2020; 11:459. [PMID: 32411158 PMCID: PMC7202288 DOI: 10.3389/fpls.2020.00459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/27/2020] [Indexed: 05/19/2023]
Abstract
The herbicide glyphosate inhibits the plant enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the aromatic amino acid (AAA) biosynthetic pathway, also known as the shikimate pathway. Amaranthus palmeri is a fast-growing weed, and several populations have evolved resistance to glyphosate through increased EPSPS gene copy number. The main objective of this study was to elucidate the regulation of the shikimate pathway and determine whether the regulatory mechanisms of glyphosate-sensitive and glyphosate-resistant plants were different. Leaf disks of sensitive and resistant (due to EPSPS gene amplification) A. palmeri plants were incubated for 24 h with glyphosate, AAA, glyphosate + AAA, or several intermediates of the pathway: shikimate, quinate, chorismate and anthranilate. In the sensitive population, glyphosate induced shikimate accumulation and induced the gene expression of the shikimate pathway. While AAA alone did not elicit any change, AAA applied with glyphosate abolished the effects of the herbicide on gene expression. It was not possible to fully mimic the effect of glyphosate by incubation with any of the intermediates, but shikimate was the intermediate that induced the highest increase (three-fold) in the expression level of the genes of the shikimate pathway of the sensitive population. These results suggest that, in this population, the lack of end products (AAA) of the shikimate pathway and shikimate accumulation would be the signals inducing gene expression in the AAA pathway after glyphosate application. In general, the effects on gene expression detected after the application of the intermediates were more severe in the sensitive population than in the resistant population. These results suggest that when EPSPS is overexpressed, as in the resistant population, the regulatory mechanisms of the AAA pathway are disrupted or buffered. The mechanisms underlying this behavior remain to be elucidated.
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Affiliation(s)
| | | | | | | | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
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21
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Perotti VE, Larran AS, Palmieri VE, Martinatto AK, Permingeat HR. Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110255. [PMID: 31779903 DOI: 10.1016/j.plantsci.2019.110255] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/16/2023]
Abstract
Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.
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Affiliation(s)
- Valeria E Perotti
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Alvaro S Larran
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Valeria E Palmieri
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Andrea K Martinatto
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Hugo R Permingeat
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina.
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22
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Fernández-Escalada M, Zulet-González A, Gil-Monreal M, Royuela M, Zabalza A. Physiological performance of glyphosate and imazamox mixtures on Amaranthus palmeri sensitive and resistant to glyphosate. Sci Rep 2019; 9:18225. [PMID: 31796801 PMCID: PMC6890711 DOI: 10.1038/s41598-019-54642-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
The herbicides glyphosate and imazamox inhibit the biosynthetic pathway of aromatic amino acids (AAA) and branched-chain amino acids (BCAA), respectively. Both herbicides share several physiological effects in the processes triggered in plants after herbicide application that kills the plant, and mixtures of both herbicides are being used. The aim of this study was to evaluate the physiological effects in the mixture of glyphosate and imazamox in glyphosate-sensitive (GS) and -resistant (GR) populations of the troublesome weed Amaranthus palmeri. The changes detected in the physiological parameters after herbicide mixtures application were similar and even less to the changes detected after individual treatments. This pattern was detected in shikimate, amino acid and carbohydrate content, and it was independent of the EPSPS copy number, as it was detected in both populations. In the case of the transcriptional pattern of the AAA pathway after glyphosate, interesting and contrary interactions with imazamox treatment were detected for both populations; enhancement of the effect in the GS population and alleviation in the GR population. At the transcriptional level, no cross regulation between AAA and BCAA inhibitors was confirmed. This study suggests that mixtures are equally or less toxic than herbicides alone, and would implicate careful considerations when applying the herbicide mixtures.
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Affiliation(s)
- Manuel Fernández-Escalada
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus Arrosadia s/n, 31006, Pamplona, Spain
| | - Ainhoa Zulet-González
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus Arrosadia s/n, 31006, Pamplona, Spain
| | - Miriam Gil-Monreal
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus Arrosadia s/n, 31006, Pamplona, Spain
| | - Mercedes Royuela
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus Arrosadia s/n, 31006, Pamplona, Spain
| | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus Arrosadia s/n, 31006, Pamplona, Spain.
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Yu J, Zhang Y, Ning S, Ye Q, Tan H, Chen R, Bu Q, Zhang R, Gong P, Ma X, Zhang L, Wei D. Molecular cloning and metabolomic characterization of the 5-enolpyruvylshikimate-3-phosphate synthase gene from Baphicacanthus cusia. BMC PLANT BIOLOGY 2019; 19:485. [PMID: 31706293 PMCID: PMC6842527 DOI: 10.1186/s12870-019-2035-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Indigo alkaloids, such as indigo, indirubin and its derivatives, have been identified as effective antiviral compounds in Baphicacanthus cusia. Evidence suggests that the biosynthesis of indigo alkaloids in plants occurs via the shikimate pathway. The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is involved in plant metabolism; however, its underlying putative mechanism of regulating the production of indigo alkaloids is currently unknown. RESULTS One gene encoding EPSPS was isolated from B. cusia. Quantitative real-time PCR analysis revealed that BcEPSPS was expressed at the highest level in the stem and upregulated by methyl jasmonate (MeJA), salicylic acid (SA) and abscisic acid (ABA) treatment. The results of subcellular localization indicated that BcEPSPS is mainly expressed in both the plastids and cytosol, which has not been previously reported. An enzyme assay revealed that the heterogeneously expressed BcEPSPS protein catalysed the generation of 5-enolpyruvyl shikimate-3-phosphate. The overexpression of BcEPSPS in Isatis indigotica hairy roots resulted in the high accumulation of indigo alkaloids, such as indigo, secologanin, indole and isorhamnetin. CONCLUSIONS The function of BcEPSPS in catalysing the production of EPSP and regulating indigo alkaloid biosynthesis was revealed, which provided a distinct view of plant metabolic engineering. Our findings have practical implications for understanding the effect of BcEPSPS on active compound biosynthesis in B. cusia.
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Affiliation(s)
- Jian Yu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
- School of Life Sciences, East China Normal University, Shanghai, 200433, People's Republic of China
| | - Yihan Zhang
- Department of Pharmaceutical Changzheng Hosipital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Shuju Ning
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Qi Ye
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Qitao Bu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Rui Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Peimin Gong
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Xiaoli Ma
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China.
| | - Daozhi Wei
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fuzhou, 350002, People's Republic of China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fuzhou, 350002, People's Republic of China.
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Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus. Proc Natl Acad Sci U S A 2019; 116:21076-21084. [PMID: 31570613 PMCID: PMC6800383 DOI: 10.1073/pnas.1900870116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
While evolution has been thought of as playing out over millions of years, adaptation to new environments can occur very rapidly, presenting us with key opportunities to understand evolutionary dynamics. One of the most amazing examples of real-time evolution comes from agriculture, where due to the intense use of a few herbicides, many plant species have evolved herbicide resistance to become aggressive weeds. An important question has been whether herbicide resistance arises only rarely and then spreads quickly, or whether herbicide resistance arises all the time de novo. Our work with glyphosate resistance in US Midwestern and Canadian populations of Amaranthus tuberculatus reveals the answer to be, “it depends,” as we surprisingly find examples for both modes of evolution. The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, or geographic spread of adaptive alleles through gene flow. Glyphosate-resistant Amaranthus tuberculatus poses one of the most significant threats to crop yields in the Midwestern United States, with both agricultural populations and herbicide resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the A. tuberculatus genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals from Canada and the United States. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically nonagricultural. Moreover, resistance on these local, nonagricultural backgrounds appears to have occurred predominantly through the partial sweep of a single haplotype. In contrast, resistant haplotypes arising from the Midwestern United States show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable species-wide diversity of A. tuberculatus has facilitated geographic parallel adaptation of glyphosate resistance, more recently established agricultural populations are limited to adaptation in a more mutation-limited framework.
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25
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Gaines TA, Patterson EL, Neve P. Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance. THE NEW PHYTOLOGIST 2019; 223:1770-1775. [PMID: 31002387 DOI: 10.1111/nph.15858] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.
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Affiliation(s)
- Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Paul Neve
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
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26
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Jiang J. Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 2019; 27:153-165. [PMID: 30852707 DOI: 10.1007/s00425-00018-03033-00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 05/20/2023]
Abstract
Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. This review intends to summarize and discuss key technical development and applications of FISH in plants since 2006. The most significant recent advance of FISH is the development and application of probes based on synthetic oligonucleotides (oligos). Oligos specific to a repetitive DNA sequence, to a specific chromosomal region, or to an entire chromosome can be computationally identified, synthesized in parallel, and fluorescently labeled. Oligo probes designed from conserved DNA sequences from one species can be used among genetically related species, allowing comparative cytogenetic mapping of these species. The advances with synthetic oligo probes will significantly expand the applications of FISH especially in non-model plant species. Recent achievements and future applications of FISH and oligo-FISH are discussed.
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Affiliation(s)
- Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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27
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Wicke D, Schulz LM, Lentes S, Scholz P, Poehlein A, Gibhardt J, Daniel R, Ischebeck T, Commichau FM. Identification of the first glyphosate transporter by genomic adaptation. Environ Microbiol 2019; 21:1287-1305. [PMID: 30666812 DOI: 10.1111/1462-2920.14534] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/12/2023]
Abstract
The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.
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Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Lisa M Schulz
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Till Ischebeck
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
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28
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Jiang J. Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 2019; 27:153-165. [PMID: 30852707 DOI: 10.1007/s10577-019-09607-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 01/20/2023]
Abstract
Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. This review intends to summarize and discuss key technical development and applications of FISH in plants since 2006. The most significant recent advance of FISH is the development and application of probes based on synthetic oligonucleotides (oligos). Oligos specific to a repetitive DNA sequence, to a specific chromosomal region, or to an entire chromosome can be computationally identified, synthesized in parallel, and fluorescently labeled. Oligo probes designed from conserved DNA sequences from one species can be used among genetically related species, allowing comparative cytogenetic mapping of these species. The advances with synthetic oligo probes will significantly expand the applications of FISH especially in non-model plant species. Recent achievements and future applications of FISH and oligo-FISH are discussed.
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Affiliation(s)
- Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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29
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First Report of Amaranthus hybridus with Multiple Resistance to 2,4-D, Dicamba, and Glyphosate. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In many countries, Amaranthus hybridus is a widespread weed in agricultural systems. The high prolificacy and invasive capacity as well as the resistance of some biotypes to herbicides are among the complications of handling this weed. This paper reports on the first A. hybridus biotypes with resistance to auxinic herbicides and multiple resistance to auxinic herbicides and the EPSPs inhibitor, glyphosate. Several dose response assays were carried out to determine and compare sensitivity of six population of A. hybridus to glyphosate, 2,4-D, and dicamba. In addition, shikimic acid accumulation and piperonil butoxide effects on 2,4-D and dicamba metabolism were tested in the same populations. The results showed four populations were resistant to dicamba and three of these were also resistant to 2,4-D, while only one population was resistant to glyphosate. The glyphosate-resistant population also showed multiple resistance to auxinic herbicides. Pretreatment with piperonil butoxide (PBO) followed by 2,4-D or dicamba resulted in the death of all individual weeds independent of herbicide or population.
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30
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Selective fertilization with phosphite allows unhindered growth of cotton plants expressing the ptxD gene while suppressing weeds. Proc Natl Acad Sci U S A 2018; 115:E6946-E6955. [PMID: 29866830 PMCID: PMC6055188 DOI: 10.1073/pnas.1804862115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An increasing number of herbicide-resistant weeds are being reported in the United States, Argentina, and Brazil. This is becoming a global challenge for the production of several major crops, such as cotton, maize, and soybean. New strategies for weed control are required to sustain agricultural production while reducing our dependence on herbicides. Here, we report that selective fertilization of transgenic cotton, expressing a bacterial phosphite dehydrogenase (PTXD), with phosphite provides an effective way to suppress weed growth. Importantly, we show that the ptxD-transgenic cotton plants successfully outcompete a highly aggressive glyphosate-resistant weed. The ptxD/phosphite system represents one of the most promising technologies of recent times with potential to solve many of the agricultural and environmental problems that we encounter currently. Weeds, which have been the bane of agriculture since the beginning of civilization, are managed manually, mechanically, and, more recently, by chemicals. However, chemical control options are rapidly shrinking due to the recent rise in the number of herbicide-resistant weeds in crop fields, with few alternatives on the horizon. Therefore, there is an urgent need for alternative weed suppression systems to sustain crop productivity while reducing our dependence on herbicides and tillage. Such a development will also allay some of the negative perceptions associated with the use of herbicide-resistance genes and heavy dependence on herbicides. Transgenic plants expressing the bacterial phosphite dehydrogenase (ptxD) gene gain an ability to convert phosphite (Phi) into orthophosphate [Pi, the metabolizable form of phosphorus (P)]. Such plants allow for a selective fertilization scheme, based on Phi as the sole source of P for the crop, while offering an effective alternative for suppressing weed growth. Here, we show that, when P is supplied in the form of Phi, ptxD-expressing cotton (Gossypium hirsutum L.) plants outcompete, in both artificial substrates and natural soils from agricultural fields, three different monocot and dicot weed species intentionally introduced in the experiments, as well as weeds naturally present in the tested soils. Importantly, the ptxD/Phi system proved highly efficacious in inhibiting the growth of glyphosate-resistant Palmer amaranth. With over 250 weed species resistant to currently available herbicides, ptxD-transgenic plants fertilized with Phi could provide an effective alternative to suppressing the growth of these weeds while providing adequate nutrition to the crop.
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31
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Sammons RD, You J, Qi Y, Flasinski S, Kavanaugh C, Washam J, Ostrander E, Wang D, Heck G. Evaluation of glyphosate resistance in Arabidopsis thaliana expressing an altered target site EPSPS. PEST MANAGEMENT SCIENCE 2018; 74:1174-1183. [PMID: 28677849 PMCID: PMC5901408 DOI: 10.1002/ps.4654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/15/2017] [Accepted: 06/21/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Glyphosate-resistant goosegrass has recently evolved and is homozygous for the double mutant of EPSPS (T102 I, P106 S or TIPS). These same mutations combined with EPSPS overexpression, have been used to create transgenic glyphosate-resistant crops. Arabidopsis thaliana (Wt EPSPS Ki ∼ 0.5 μM) was engineered to express a variant AtEPSPS-T102 I, P106 A (TIPA Ki = 150 μM) to determine the resistance magnitude for a more potent variant EPSPS that might evolve in weeds. RESULTS Transgenic A. thaliana plants, homozygous for one, two or four copies of AtEPSPS-TIPA, had resistance (IC50 values, R/S) as measured by seed production ranging from 4.3- to 16-fold. Plants treated in reproductive stage were male sterile with a range of R/S from 10.1- to 40.6-fold. A significant hormesis (∼ 63% gain in fresh weight) was observed for all genotypes when treated at the initiation of reproductive stage with 0.013 kg ha-1 . AtEPSPS-TIPA enzyme activity was proportional to copy number and correlated with resistance magnitude. CONCLUSIONS A. thaliana, as a model weed expressing one copy of AtEPSPS-TIPA (300-fold more resistant), had only 4.3-fold resistance to glyphosate for seed production. Resistance behaved as a single dominant allele. Vegetative tissue resistance was 4.7-fold greater than reproductive tissue resistance and was linear with gene copy number. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | | | | | | | | | | | - Elizabeth Ostrander
- Division of Oncology, Section of Oncology, Department of Internal MedicineWashington University in St LouisSt LouisMissouriUSA
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32
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Kreiner JM, Stinchcombe JR, Wright SI. Population Genomics of Herbicide Resistance: Adaptation via Evolutionary Rescue. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:611-635. [PMID: 29140727 DOI: 10.1146/annurev-arplant-042817-040038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The evolution of herbicide resistance in weed populations is a highly replicated example of adaptation surmounting the race against extinction, but the factors determining its rate and nature remain poorly understood. Here, we explore theory and empirical evidence for the importance of population genetic parameters-including effective population size, dominance, mutational target size, and gene flow-in influencing the probability and mode of herbicide resistance adaptation and its variation across species. We compiled data on the number of resistance mutations across populations for 79 herbicide-resistant species. Our findings are consistent with theoretical predictions that self-fertilization reduces resistance adaptation from standing variation within populations, but increases independent adaptation across populations. Furthermore, we provide evidence for a ploidy-mating system interaction that may reflect trade-offs in polyploids between increased effective population size and greater masking of beneficial mutations. We highlight the power of population genomic approaches to provide insights into the evolutionary dynamics of herbicide resistance with important implications for understanding the limits of adaptation.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
| | | | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
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33
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Koo DH, Molin WT, Saski CA, Jiang J, Putta K, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc Natl Acad Sci U S A 2018; 115:3332-3337. [PMID: 29531028 PMCID: PMC5879691 DOI: 10.1073/pnas.1719354115] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - William T Molin
- Crop Production Systems Research Unit, US Department of Agriculture-Agricultural Research Services, Stoneville, MS 38776
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506;
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34
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Koo DH, Jugulam M, Putta K, Cuvaca IB, Peterson DE, Currie RS, Friebe B, Gill BS. Gene Duplication and Aneuploidy Trigger Rapid Evolution of Herbicide Resistance in Common Waterhemp. PLANT PHYSIOLOGY 2018; 176:1932-1938. [PMID: 29295942 PMCID: PMC5841708 DOI: 10.1104/pp.17.01668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/27/2017] [Indexed: 05/25/2023]
Abstract
An increase in gene copy number is often associated with changes in the number and structure of chromosomes, as has been widely observed in yeast and eukaryotic tumors, yet little is known about stress-induced chromosomal changes in plants. Previously, we reported that the EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene, the molecular target of glyphosate, was amplified at the native locus and on an extra chromosome in glyphosate-resistant Amaranthus tuberculatus Here, we report that the extra chromosome is a ring chromosome termed extra circular chromosome carrying amplified EPSPS (ECCAE). The ECCAE is heterochromatic, harbors four major EPSPS amplified foci, and is sexually transmitted to 35% of the progeny. Two highly glyphosate resistant (HGR) A. tuberculatus plants with a chromosome constitution of 2n = 32+1 ECCAE displayed soma cell heterogeneity. Some cells had secondary ECCAEs, which displayed size polymorphisms and produced novel chromosomal variants with multiple gene amplification foci. We hypothesize that the ECCAE in the soma cells of HGR A. tuberculatus plants underwent breakage-fusion-bridge cycles to generate the observed soma cell heterogeneity, including de novo EPSPS gene integration into chromosomes. Resistant soma cells with stable EPSPS amplification events as de novo insertions into chromosomes may survive glyphosate selection pressure during the sporophytic phase and are plausibly transmitted to germ cells leading to durable glyphosate resistance in A. tuberculatus This is the first report of early events in aneuploidy-triggered de novo chromosome integration by an as yet unknown mechanism, which may drive rapid adaptive evolution of herbicide resistance in common waterhemp.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Mithila Jugulam
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Karthik Putta
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Ivan B Cuvaca
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Dallas E Peterson
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Randall S Currie
- Southwest Research and Extension Center, Garden City, Kansas State University, Manhattan, Kansas 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
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Yu Y. A Novel Role of Ring Chromosomes as Evolutionary Drivers of Herbicide Resistance. PLANT PHYSIOLOGY 2018; 176:1892-1893. [PMID: 29630499 PMCID: PMC5841723 DOI: 10.1104/pp.18.00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Patterson EL, Pettinga DJ, Ravet K, Neve P, Gaines TA. Glyphosate Resistance and EPSPS Gene Duplication: Convergent Evolution in Multiple Plant Species. J Hered 2018; 109:117-125. [PMID: 29040588 DOI: 10.1093/jhered/esx087] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022] Open
Abstract
One of the increasingly widespread mechanisms of resistance to the herbicide glyphosate is copy number variation (CNV) of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. EPSPS gene duplication has been reported in 8 weed species, ranging from 3 to 5 extra copies to more than 150 extra copies. In the case of Palmer amaranth (Amaranthus palmeri), a section of >300 kb containing EPSPS and many other genes has been replicated and inserted at new loci throughout the genome, resulting in significant increase in total genome size. The replicated sequence contains several classes of mobile genetic elements including helitrons, raising the intriguing possibility of extra-chromosomal replication of the EPSPS-containing sequence. In kochia (Kochia scoparia), from 3 to more than 10 extra EPSPS copies are arranged as a tandem gene duplication at one locus. In the remaining 6 weed species that exhibit EPSPS gene duplication, little is known about the underlying mechanisms of gene duplication or their entire sequence. There is mounting evidence that adaptive gene amplification is an important mode of evolution in the face of intense human-mediated selection pressure. The convergent evolution of CNVs for glyphosate resistance in weeds, through at least 2 different mechanisms, may be indicative of a more general importance for this mechanism of adaptation in plants. CNVs warrant further investigation across plant functional genomics for adaptation to biotic and abiotic stresses, particularly for adaptive evolution on rapid time scales.
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Affiliation(s)
- Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins
| | - Dean J Pettinga
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins
| | - Karl Ravet
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins
| | - Paul Neve
- Rothamsted Research, Biointeractions and Crop Protection Department, West Common, Harpenden, Hertfordshire, UK
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins
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Wu C, Davis AS, Tranel PJ. Limited fitness costs of herbicide-resistance traits in Amaranthus tuberculatus facilitate resistance evolution. PEST MANAGEMENT SCIENCE 2018; 74:293-301. [PMID: 28834134 DOI: 10.1002/ps.4706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The fitness cost of herbicide resistance (HR) in the absence of herbicide selection plays a key role in HR evolution. Quantifying the fitness cost of resistance, however, is challenging, and there exists a knowledge gap in this area. A synthetic (artificially generated) Amaranthus tuberculatus population segregating for five types of HR was subjected to competitive growth conditions in the absence of herbicide selection for six generations. Fitness costs were quantified by using a combination of phenotyping and genotyping to monitor HR frequency changes over generations. RESULTS In the absence of herbicide selection, a significant fitness cost was observed for resistance to acetolactate synthase-inhibiting herbicides, but not for resistances to atrazine (non-target-site resistance mechanism), protoporphyrinogen oxidase inhibitors, 4-hydroxyphenylpryuvate dioxygenase inhibitors or glyphosate. Glyphosate resistance was conferred by multiple mechanisms in the synthetic population, and further analysis revealed that one mechanism, amplification of the 5-enolypyruvylshikimate-3-phosphate synthase gene, did decrease in frequency. CONCLUSION Our results indicate that herbicide-resistance mitigation strategies (e.g. herbicide rotation) that rely on the existence of fitness costs in the absence of herbicide selection likely will be largely ineffective in many cases. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Chenxi Wu
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Adam S Davis
- USDA-ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Jugulam M, Gill BS. Molecular cytogenetics to characterize mechanisms of gene duplication in pesticide resistance. PEST MANAGEMENT SCIENCE 2018; 74:22-29. [PMID: 28714247 DOI: 10.1002/ps.4665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular cytogenetics empower construction of physical maps to illustrate the precise position of genetic loci on the chromosomes. Such maps provide visible information about the position of DNA sequences, including the distribution of repetitive sequences on the chromosomes. This is an important step toward unraveling the genetic mechanisms implicated in chromosomal aberrations (e.g., gene duplication). In response to stress, such as pesticide selection, duplicated genes provide an immediate adaptive advantage to organisms that overcome unfavorable conditions. Although the significance of gene duplication as one of the important events driving genetic diversity has been reported, the precise mechanisms of gene duplication that contribute to pesticide resistance, especially to herbicides, are elusive. With particular reference to pesticide resistance, we discuss the prospects of application of molecular cytogenetic tools to uncover mechanism(s) of gene duplication, and illustrate hypothetical models that predict the evolutionary basis of gene duplication. The cytogenetic basis of duplicated genes, their stability, as well as the magnitude of selection pressure, can determine the dynamics of the genetic locus (loci) conferring pesticide resistance not only at the population level, but also at the individual level. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Mithila Jugulam
- Department of Agronomy Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Fernández-Escalada M, Zulet-González A, Gil-Monreal M, Zabalza A, Ravet K, Gaines T, Royuela M. Effects of EPSPS Copy Number Variation (CNV) and Glyphosate Application on the Aromatic and Branched Chain Amino Acid Synthesis Pathways in Amaranthus palmeri. FRONTIERS IN PLANT SCIENCE 2017; 8:1970. [PMID: 29201035 PMCID: PMC5696356 DOI: 10.3389/fpls.2017.01970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/01/2017] [Indexed: 05/09/2023]
Abstract
A key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), is the known target of the widely used herbicide glyphosate. Glyphosate resistance in Amaranthus palmeri, one of the most troublesome weeds in agriculture, has evolved through increased EPSPS gene copy number. The aim of this work was to study the pleiotropic effects of (i) EPSPS increased transcript abundance due to gene copy number variation (CNV) and of (ii) glyphosate application on the aromatic amino acid (AAA) and branched chain amino acid (BCAA) synthesis pathways. Hydroponically grown glyphosate sensitive (GS) and glyphosate resistant (GR) plants were treated with glyphosate 3 days after treatment. In absence of glyphosate treatment, high EPSPS gene copy number had only a subtle effect on transcriptional regulation of AAA and BCAA pathway genes. In contrast, glyphosate treatment provoked a general accumulation of the transcripts corresponding to genes of the AAA pathway leading to synthesis of chorismate in both GS and GR. After chorismate, anthranilate synthase transcript abundance was higher while chorismate mutase transcription showed a small decrease in GR and remained stable in GS, suggesting a regulatory branch point in the pathway that favors synthesis toward tryptophan over phenylalanine and tyrosine after glyphosate treatment. This was confirmed by studying enzyme activities in vitro and amino acid analysis. Importantly, this upregulation was glyphosate dose dependent and was observed similarly in both GS and GR populations. Glyphosate treatment also had a slight effect on the expression of BCAA genes but no general effect on the pathway could be observed. Taken together, our observations suggest that the high CNV of EPSPS in A. palmeri GR populations has no major pleiotropic effect on the expression of AAA biosynthetic genes, even in response to glyphosate treatment. This finding supports the idea that the fitness cost associated with EPSPS CNV in A. palmeri may be limited.
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Affiliation(s)
| | - Ainhoa Zulet-González
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
| | - Miriam Gil-Monreal
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
| | - Ana Zabalza
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
| | - Karl Ravet
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Todd Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Royuela
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
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Laforest M, Soufiane B, Simard MJ, Obeid K, Page E, Nurse RE. Acetyl-CoA carboxylase overexpression in herbicide-resistant large crabgrass (Digitaria sanguinalis). PEST MANAGEMENT SCIENCE 2017; 73:2227-2235. [PMID: 28755464 DOI: 10.1002/ps.4675] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND The occurrence of herbicide-resistant weed biotypes is increasing and this report of an acetyl-CoA carboxylase (ACCase) inhibitor-resistant Digitaria sanguinalis L. Scop. from southwestern Ontario is another example. The identified weed escaped control in an onion and carrot rotation in which graminicides were used for several consecutive years. Our goal was to characterize the level and mechanism of resistance of the biotype. RESULTS The biotype was resistant to all five ACCase inhibitor herbicides tested. Gene-expression profiling was performed because none of the mutations known to confer resistance in the ACCase gene were detected. RNASeq and quantitative reverse-transcriptase PCR (qRT-PCR) results indicated that transcription of ACCase was 3.4-9.3 times higher in the resistant biotype than the susceptible biotype. ACCase gene copy number was determined by qPCR to be five to seven times higher in the resistant compared with the susceptible biotype. ACCase gene overexpression was directly related to the increase of the ACCase gene copy number. CONCLUSION Our results are consistent with the hypothesis that overexpression of the herbicide target gene ACCase confers resistance to the herbicide. This is the first reported case of target gene duplication conferring resistance to a herbicide other than glyphosate. © 2017 Society of Chemical Industry See related Article.
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Affiliation(s)
- Martin Laforest
- Agriculture and Agri-Food Canada (AAFC), Saint-Jean-sur-Richelieu Research and Development Centre, St-Jean-sur-Richelieu, Québec, Canada
| | - Brahim Soufiane
- Agriculture and Agri-Food Canada (AAFC), Saint-Jean-sur-Richelieu Research and Development Centre, St-Jean-sur-Richelieu, Québec, Canada
| | - Marie-Josée Simard
- Agriculture and Agri-Food Canada (AAFC), Saint-Jean-sur-Richelieu Research and Development Centre, St-Jean-sur-Richelieu, Québec, Canada
| | - Kristen Obeid
- Ontario Ministry of Agriculture, Food and Rural Affairs, Harrow Research and Development Centre, Harrow, Ontario, Canada
| | - Eric Page
- Agriculture and Agri-Food Canada (AAFC), Harrow Research and Development Centre, Harrow, Ontario, Canada
| | - Robert E Nurse
- Agriculture and Agri-Food Canada (AAFC), Harrow Research and Development Centre, Harrow, Ontario, Canada
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Tranel PJ. Herbicide-resistance mechanisms: gene amplification is not just for glyphosate. PEST MANAGEMENT SCIENCE 2017; 73:2225-2226. [PMID: 28755431 DOI: 10.1002/ps.4679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
See related Article
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Affiliation(s)
- Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Champaign, IL, USA
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Iwakami S, Shimono Y, Manabe Y, Endo M, Shibaike H, Uchino A, Tominaga T. Copy Number Variation in Acetolactate Synthase Genes of Thifensulfuron-Methyl Resistant Alopecurus aequalis (Shortawn Foxtail) Accessions in Japan. FRONTIERS IN PLANT SCIENCE 2017; 8:254. [PMID: 28303143 PMCID: PMC5332366 DOI: 10.3389/fpls.2017.00254] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/09/2017] [Indexed: 05/22/2023]
Abstract
Severe infestations of Alopecurus aequalis (shortawn foxtail), a noxious weed in wheat and barley cropping systems in Japan, can occur even after application of thifensulfuron-methyl, a sulfonylurea (SU) herbicide. In the present study, nine accessions of A. aequalis growing in a single wheat field were tested for sensitivity to thifensulfuron-methyl. Seven of the nine accessions survived application of standard field rates of thifensulfuron-methyl, indicating that severe infestations likely result from herbicide resistance. Acetolactate synthase (ALS) is the target enzyme of SU herbicides. Full-length genes encoding ALS were therefore isolated to determine the mechanism of SU resistance. As a result, differences in ALS gene copy numbers among accessions were revealed. Two copies, ALS1 and ALS2, were conserved in all accessions, while some carried two additional copies, ALS3 and ALS4. A single-base deletion in ALS3 and ALS4 further indicated that they represent pseudogenes. No differences in ploidy level were observed between accessions with two or four copies of the ALS gene, suggesting that copy number varies. Resistant plants were found to carry a mutation in either the ALS1 or ALS2 gene, with all mutations causing an amino acid substitution at the Pro197 residue, which is known to confer SU resistance. Transcription of each ALS gene copy was confirmed by reverse transcription PCR, supporting involvement of these mutations in SU resistance. The information on the copy number and full-length sequences of ALS genes in A. aequalis will aid future analysis of the mechanism of resistance.
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Affiliation(s)
- Satoshi Iwakami
- Graduate School of Agriculture, Kyoto UniversityKyoto, Japan
- Crop Production Systems Division, NARO Agricultural Research CenterTsukuba, Japan
- Faculty of Life and Environmental Sciences, University of TsukubaTsukuba, Japan
- *Correspondence: Satoshi Iwakami,
| | - Yoshiko Shimono
- Graduate School of Agriculture, Kyoto UniversityKyoto, Japan
| | - Yohei Manabe
- Graduate School of Agriculture, Kyoto UniversityKyoto, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukuba, Japan
| | | | - Akira Uchino
- Crop Production Systems Division, NARO Agricultural Research CenterTsukuba, Japan
- Central Region Agricultural Research Center, National Agriculture and Food Research OrganizationTsu, Japan
| | - Tohru Tominaga
- Graduate School of Agriculture, Kyoto UniversityKyoto, Japan
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