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Garnault M, Duplaix C, Leroux P, Couleaud G, David O, Walker AS, Carpentier F. Large-scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogen Zymoseptoria tritici in France. THE NEW PHYTOLOGIST 2021; 229:3508-3521. [PMID: 33226662 DOI: 10.1111/nph.17107] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale. We focused on Zymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25 000 km2 on average). We modelled changes in resistance frequency with regional anti-Septoria fungicide use, yield losses due to the disease and the regional area under organic wheat. The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R2 from 0.56 to 0.82). The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions.
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Affiliation(s)
- Maxime Garnault
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Clémentine Duplaix
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Pierre Leroux
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | | | - Olivier David
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Anne-Sophie Walker
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Florence Carpentier
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
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Ding S, Meinholz K, Cleveland K, Jordan SA, Gevens AJ. Diversity and Virulence of Alternaria spp. Causing Potato Early Blight and Brown Spot in Wisconsin. PHYTOPATHOLOGY 2019; 109:436-445. [PMID: 30256185 DOI: 10.1094/phyto-06-18-0181-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Early blight, caused by Alternaria solani, along with brown spot, caused by A. alternata, have the potential to reduce quality and yield in potato production globally. Prior to this study, the incidence, disease impact, and fungicide resistance attributes of A. alternata in Wisconsin were poorly understood. Potato pathogens were isolated from foliar lesions at three commercial locations in Wisconsin in 2012 and 2017 and were initially morphologically identified as A. solani (n = 33) and A. alternata (n = 40). Identifications were further corroborated with the phylogenetic analysis of the internal transcribed spacer (ITS), translation elongation factor 1 (TEF1), gapdh, Alt a 1, and OPA10-2. A multigene phylogeny of ITS, TEF1, gapdh, and Alt a 1 showed five genotypes of A. alternata and one single genotype of A. solani. We demonstrated that the A. alternata isolates were virulent on potato cultivars Russet Burbank (P < 0.013) and Atlantic (P < 0.0073), though they caused less disease than A. solani (P < 0.0001 and P < 0.0001, respectively). A. alternata caused little disease on the breeding line 24-24-12 (P = 0.9929), and A. solani caused fewer disease symptoms on 24-24-12 than on Russet Burbank (P < 0.0001) or Atlantic (P < 0.0001). Breeding line 24-24-12 may be a promising source of potential resistance for the two diseases. There was no significant difference in virulence of different A. alternata genotypes, and no significant difference in virulence or genotype clustering among isolates from the three locations. Isolates of A. alternata that induced chlorosis caused larger lesion areas than isolates that did not in Russet Burbank (P < 0.0001), Atlantic (P < 0.0001), and 24-24-12 (P = 0.0365). There was no significant difference in virulence between quinone outside inhibitor (QoI)-sensitive and QoI-resistant isolates of A. alternata. This study enhanced our understanding of potato early blight and brown spot in Wisconsin, and suggested that A. alternata in addition to A. solani should be carefully monitored and possibly uniquely managed in order to achieve overall disease control.
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Affiliation(s)
- Shunping Ding
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison 53706
| | - Kiana Meinholz
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison 53706
| | - Kenneth Cleveland
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison 53706
| | - Stephen A Jordan
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison 53706
| | - Amanda J Gevens
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison 53706
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Hawkins NJ, Fraaije BA. Fitness Penalties in the Evolution of Fungicide Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:339-360. [PMID: 29958074 DOI: 10.1146/annurev-phyto-080417-050012] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The evolution of resistance poses an ongoing threat to crop protection. Fungicide resistance provides a selective advantage under fungicide selection, but resistance-conferring mutations may also result in fitness penalties, resulting in an evolutionary trade-off. These penalties may result from the functional constraints of an evolving target site or from the resource allocation costs of overexpression or active transport. The extent to which such fitness penalties are present has important implications for resistance management strategies, determining whether resistance persists or declines between treatments, and for resistance risk assessments for new modes of action. Experimental results have proven variable, depending on factors such as temperature, nutrient status, osmotic or oxidative stress, and pathogen life-cycle stage. Functional genetics tools allow pathogen genetic background to be controlled, but this in turn raises the question of epistatic interactions. Combining fitness penalties under various conditions into a field-realistic scenario poses an important future challenge.
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Affiliation(s)
- N J Hawkins
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
| | - B A Fraaije
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Hagerty CH, Graebner RC, Sackett KE, Mundt CC. Variable competitive effects of fungicide resistance in field experiments with a plant pathogenic fungus. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:1305-1316. [PMID: 28266146 DOI: 10.1002/eap.1524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Classic evolutionary theory suggests that mutations associated with antimicrobial and pesticide resistance result in a fitness cost in the absence of the selective antimicrobial agent or pesticide. There is experimental evidence to support fitness costs associated with resistance to anti-microbial compounds and pesticides across many biological disciplines, including human pathology, entomology, plant sciences, and plant pathology. However, researchers have also found examples of neutral and increased fitness associated with resistance, where the effect of a given resistance mutation depends on environmental and biological factors. We used Zymoseptoria tritici, a model evolutionary plant pathogenic fungus, to compare the competitive ability of fungicide-resistant isolates to fungicide-sensitive isolates. We conducted four large-scale inoculated winter wheat experiments at Oregon State University agriculture experiment stations. We found a significant change in the frequency of fungicide resistance over time in all four experiments. The direction and magnitude of these changes, however, differed by experimental location, year of experiment, and inoculum resistance treatment (fungicide-resistant, resistant/sensitive mixture, and fungicide-sensitive). These results suggest that the competitive ability of resistant isolates relative to sensitive isolates varied depending upon environmental conditions, including the initial frequency of resistant individuals in the population.
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Affiliation(s)
- Christina H Hagerty
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Road, Adams, OR, 97801, USA
| | - Ryan C Graebner
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1st St, Hermiston, OR, 97838, USA
| | - Kathryn E Sackett
- Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Christopher C Mundt
- Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, 2701 SW Campus Way, Corvallis, OR, 97331, USA
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Hagerty CH, Anderson NP, Mundt CC. Temporal Dynamics and Spatial Variation of Azoxystrobin and Propiconazole Resistance in Zymoseptoria tritici: A Hierarchical Survey of Commercial Winter Wheat Fields in the Willamette Valley, Oregon. PHYTOPATHOLOGY 2017; 107:345-352. [PMID: 27827010 DOI: 10.1094/phyto-06-16-0237-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fungicide resistance can cause disease control failure in agricultural systems, and is particularly concerning with Zymoseptoria tritici, the causal agent of Septoria tritici blotch of wheat. In North America, the first quinone outside inhibitor resistance in Z. tritici was discovered in the Willamette Valley of Oregon in 2012, which prompted this hierarchical survey of commercial winter wheat fields to monitor azoxystrobin- and propiconazole-resistant Z. tritici. Surveys were conducted in June 2014, January 2015, May 2015, and January 2016. The survey was organized in a hierarchical scheme: regions within the Willamette Valley, fields within the region, transects within the field, and samples within the transect. Overall, frequency of azoxystrobin-resistant isolates increased from 63 to 93% from June 2014 to January 2016. Resistance to azoxystrobin increased over time even within fields receiving no strobilurin applications. Propiconazole sensitivity varied over the course of the study but, overall, did not significantly change. Sensitivity to both fungicides showed no regional aggregation within the Willamette Valley. Greater than 80% of spatial variation in fungicide sensitivity was at the smallest hierarchical scale (within the transect) of the survey for both fungicides, and the resistance phenotypes were randomly distributed within sampled fields. Results suggest a need for a better understanding of the dynamics of fungicide resistance at the landscape level.
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Affiliation(s)
- Christina H Hagerty
- First author: Department of Botany and Plant Pathology, Columbia Basin Agricultural Research Center, 48037 Tubbs Ranch Road, Adams, OR 97801; second author: Department of Crop and Soil Science, Oregon State University, 2050 NE Lafayette Ave., McMinnville 97128; and third author: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, 2701 SW Campus Way, Corvallis 97331
| | - Nicole P Anderson
- First author: Department of Botany and Plant Pathology, Columbia Basin Agricultural Research Center, 48037 Tubbs Ranch Road, Adams, OR 97801; second author: Department of Crop and Soil Science, Oregon State University, 2050 NE Lafayette Ave., McMinnville 97128; and third author: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, 2701 SW Campus Way, Corvallis 97331
| | - Christopher C Mundt
- First author: Department of Botany and Plant Pathology, Columbia Basin Agricultural Research Center, 48037 Tubbs Ranch Road, Adams, OR 97801; second author: Department of Crop and Soil Science, Oregon State University, 2050 NE Lafayette Ave., McMinnville 97128; and third author: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, 2701 SW Campus Way, Corvallis 97331
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Mohd-Assaad N, McDonald BA, Croll D. Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations. Mol Ecol 2016; 25:6124-6142. [PMID: 27859799 DOI: 10.1111/mec.13916] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/13/2023]
Abstract
Evolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene (CYP51) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CYP51 mutations and the mechanisms leading to CYP51-independent resistance are poorly understood. We used whole-genome sequencing and genome-wide association studies (GWAS) to perform an unbiased screen of azole resistance loci in Rhynchosporium commune, the causal agent of the barley scald disease. We assayed cyproconazole resistance in 120 isolates collected from nine populations worldwide. We found that mutations in highly conserved genes encoding the vacuolar cation channel YVC1, a transcription activator, and a saccharopine dehydrogenase made significant contributions to fungicide resistance. These three genes were not previously known to confer resistance in plant pathogens. However, YVC1 is involved in a conserved stress response pathway known to respond to azoles in human pathogenic fungi. We also performed GWAS to identify genetic polymorphism linked to fungal growth rates. We found that loci conferring increased fungicide resistance were negatively impacting growth rates, suggesting that fungicide resistance evolution imposed costs. Analyses of population structure showed that resistance mutations were likely introduced into local populations through gene flow. Multilocus resistance evolution to fungicides shows how pathogen populations can evolve a complex genetic architecture for an important phenotypic trait within a short time span.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland
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