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Hellin P, Duvivier M, Heick TM, Fraaije BA, Bataille C, Clinckemaillie A, Legrève A, Jørgensen LN, Andersson B, Samils B, Rodemann B, Berg G, Hutton F, Garnault M, El Jarroudi M, Couleaud G, Kildea S. Spatio-temporal distribution of DMI and SDHI fungicide resistance of Zymoseptoria tritici throughout Europe based on frequencies of key target-site alterations. Pest Manag Sci 2021; 77:5576-5588. [PMID: 34392616 DOI: 10.1002/ps.6601] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Over the past decade, demethylation inhibitor (DMI) and succinate dehydrogenase inhibitor (SDHI) fungicides have been extensively used to control to septoria tritici blotch, caused by Zymoseptoria tritici on wheat. This has led to the development and selection of alterations in the target-site enzymes (CYP51 and SDH, respectively). RESULTS Taking advantage of newly and previously developed qPCR assays, the frequency of key alterations associated with DMI (CYP51-S524T) and SDHI (SDHC-T79N/I, C-N86S and C-H152R) resistance was assessed in Z. tritici-infected wheat leaf samples collected from commercial crops (n = 140) across 14 European countries prior to fungicide application in the spring of 2019. This revealed the presence of a West to East gradient in the frequencies of the most common key alterations conferring azole (S524T) and SDHI resistance (T79N and N86S), with the highest frequencies measured in Ireland and Great Britain. These observations were corroborated by sequencing (CYP51 and SDH subunits) and sensitivity phenotyping (prothioconazole-desthio and fluxapyroxad) of Z. tritici isolates collected from a selection of field samples. Additional sampling made at the end of the 2019 season confirmed the continued increase in frequency of the targeted alterations. Investigations on historical leaf DNA samples originating from different European countries revealed that the frequency of all key alterations (except C-T79I) has been gradually increasing over the past decade. CONCLUSION Whilst these alterations are quickly becoming dominant in Ireland and Great Britain, scope still exists to delay their selection throughout the wider European population, emphasizing the need for the implementation of fungicide antiresistance measures. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Pierre Hellin
- Plant and Forest Health Unit, Walloon Agricultural Research Center, Gembloux, Belgium
| | - Maxime Duvivier
- Plant and Forest Health Unit, Walloon Agricultural Research Center, Gembloux, Belgium
| | - Thies M Heick
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Charlotte Bataille
- Plant and Forest Health Unit, Walloon Agricultural Research Center, Gembloux, Belgium
| | | | - Anne Legrève
- Applied Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Björn Andersson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bernd Rodemann
- Department of Mycology and Virology, Julius Kühn-Institut, Braunschweig, Germany
| | - Gunilla Berg
- Plant Protection Centre, Swedish Board of Agriculture, Alnarp, Sweden
| | - Fiona Hutton
- Teagasc, The Agriculture and Food Development Authority, Carlow, Ireland
| | - Maxime Garnault
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, France
| | - Moussa El Jarroudi
- Department of Environmental Sciences and Management, University of Liège, Arlon Campus Environnement, Arlon, Belgium
| | | | - Steven Kildea
- Teagasc, The Agriculture and Food Development Authority, Carlow, Ireland
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Samils B, Andersson B, Edin E, Elfstrand M, Rönneburg T, Bucur D, Hutton F, Heick TM, Hellin P, Kildea S. Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici. Front Microbiol 2021; 12:692845. [PMID: 34234765 PMCID: PMC8256687 DOI: 10.3389/fmicb.2021.692845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
Fungicide resistance has become a challenging problem in management of Septoria tritici blotch (STB), caused by Zymoseptoria tritici, the most destructive disease of winter wheat throughout western and northern Europe. To ensure the continued effectiveness of those fungicides currently used, it is essential to monitor the development and spread of such resistance in field populations of the pathogen. Since resistance to the key families of fungicides used for STB control (demethyalation inhibitors or azoles, succinate dehydrogenase inhibitors or SDHIs and Quinone outside Inhibitors or QoIs) is conferred through target-site mutations, the potential exists to monitor resistance through the molecular detection of alterations in the target site genes. As more efficient fungicides were developed and applied, the pathogen has continuously adapted through accumulating multiple target-site alterations. In order to accurately monitor these changes in field populations, it is therefore becoming increasingly important to completely sequence the targeted genes. Here we report the development of a PacBio assay that facilitates the multiplex amplification and long-read sequencing of the target gene(s) for the azole (CYP51), SDHI (Sdh B, C, and D), and QoI (cytochrome b) fungicides. The assay was developed and optimised using three Irish Z. tritici collections established in spring 2017, which capture the range of fungicide resistance present in modern European populations of Z. tritici. The sequences obtained through the PacBio assay were validated using traditional Sanger sequencing and in vitro sensitivity screenings. To further exploit the long-read and high throughput potential of PacBio sequencing, an additional nine housekeeping genes (act, BTUB, cal, cyp, EF1, GAPDH, hsp80-1, PKC, TFC1) were sequenced and used to provide comprehensive Z. tritici strain genotyping.
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Affiliation(s)
- Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Andersson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Eva Edin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tilman Rönneburg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diana Bucur
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
| | - Fiona Hutton
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
| | - Thies M. Heick
- Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Pierre Hellin
- Plant and Forest Health Unit, Walloon Agricultural Research Center, Gembloux, Belgium
| | - Steven Kildea
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
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Samils B, Kaitera J, Persson T, Stenlid J, Barklund P. Relationship and genetic structure among autoecious and heteroecious populations of Cronartium pini in northern Fennoscandia. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Capador H, Samils B, Kaitera J, Olson Å. Genetic evidence for sexual reproduction and multiple infections of Norway spruce cones by the rust fungus Thekopsora areolata. Ecol Evol 2020; 10:7389-7403. [PMID: 32760536 PMCID: PMC7391340 DOI: 10.1002/ece3.6466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 11/06/2022] Open
Abstract
Rust fungi are obligate parasites, of plants, with complex and in many cases poorly known life cycles which may include host alteration and up to five spore types with haploid, diploid, and dikaryotic nuclear stages. This study supports that Thekopasora areolata, the causal agent of cherry-spruce rust in Norway spruce, is a macrocyclic heteroecious fungus with all five spore stages which uses two host plants Prunus padus and Picea abies to complete its life cycle. High genotypic diversity without population structure was found, which suggests predominantly sexual reproduction, random mating and a high gene flow within and between the populations in Fennoscandia. There was no evidence for an autoecious life cycle resulting from aeciospore infection of pistillate cones that would explain the previously reported rust epidemics without the alternate host. However, within cones and scales identical multilocus genotypes were repeatedly sampled which can be explained by vegetative growth of the fertilized mycelia or repeated mating of mycelium by spermatia of the same genotype. The high genotypic diversity within cones and haplotype inference show that each pistillate cone is infected by several basidiospores. This study provides genetic evidence for high gene flow, sexual reproduction, and multiple infections of Norway spruce cone by the rust fungus T. areolata which expands the general understanding of the biology of rust fungi.
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Affiliation(s)
- Hernán Capador
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Berit Samils
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Juha Kaitera
- Natural Resources Institute FinlandUniversity of OuluOuluFinland
| | - Åke Olson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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Berlin A, Samils B, Andersson B. Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi. Fungal Biol Biotechnol 2017; 4:3. [PMID: 28955472 PMCID: PMC5611640 DOI: 10.1186/s40694-017-0032-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cereal rust fungi (Puccinia spp.) are among the most economically important plant pathogens. These fungi have a complex life cycle, including five spore stages and two hosts. They infect one grass host on which they reproduce clonally and cause the cereal rust diseases, while the alternate host is required for sexual reproduction. Although previous studies clearly demonstrate the importance of the alternate host in creating genetic diversity in cereal rust fungi, little is known about the amount of novel genotypes created in each successful completion of a sexual reproduction event. RESULTS In this study, single sequence repeat markers were used to study the genotypic diversity within aecial clusters by genotyping individual aecial cups. Two common cereal rusts, Puccinia graminis causing stem rust and Puccinia coronata the causal agent of crown rust were investigated. We showed that under natural conditions, a single aecial cluster usually include several genotypes, either because a single pycnial cluster is fertilized by several different pycniospores, or because aecia within the cluster are derived from more than one fertilized adjoining pycnial cluster, or a combination of both. CONCLUSION Our results imply that although sexual events in cereal rust fungi in most regions of the world are relatively rare, the events that occur may still significantly contribute to the genetic variation within the pathogen populations.
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Affiliation(s)
- Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Björn Andersson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
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Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B. Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix. PLoS One 2016; 11:e0168776. [PMID: 28002449 PMCID: PMC5176316 DOI: 10.1371/journal.pone.0168776] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022] Open
Abstract
An earlier identified major quantitative trait locus for resistance towards the willow leaf rust fungus Melampsora larici-epitea in a Salix viminalis x (S. viminalis × S. schwerinii) population was used to identify potential resistance genes to the rust pathogen. Screening a genomic bacterial artificial chromosome library with markers from the peak position of the QTL region revealed one gene with TIR-NBS-LRR (Toll Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat) domain structure indicative of a resistance gene. The resistance gene analog was denoted RGA1 and further analysis revealed a number of non-synonymous single nucleotide polymorphisms in the LRR domain between the resistant and susceptible Salix genotypes. Gene expression levels under controlled conditions showed a significantly lower constitutive expression of RGA1 in the susceptible genotype. In addition, the susceptible genotype showed a significantly reduced expression level of the RGA1 gene at 24 hours post inoculation with M. larici-epitea. This indicates that the pathogen may actively suppress RGA1 gene expression allowing a compatible plant-pathogen interaction and causing infection.
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Affiliation(s)
- Tom Martin
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Abstract
Puccinia graminis, the causal agent of stem rust, was collected from its alternate host barberry (Berberis spp.) and two different uredinial hosts, oats (Avena sativa) and rye (Secale cereale). The samples were analyzed using 11 polymorphic simple sequence repeat (SSR) markers. There were large differences between fungal populations on oats (P. graminis f. sp. avenae) and rye (P. graminis f. sp. secalis), and the genetic variation within the different formae speciales was also high. It was possible to distinguish between the two formae speciales on barberry. Additional genotypic groups not present in the field samples from oats and rye were also identified on barberry. Our results confirm the importance of barberry in maintaining the populations of P. graminis in Sweden and the importance of the sexual stage for the survival of the pathogen.
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Affiliation(s)
- Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Samils B, Ihrmark K, Kaitera J, Stenlid J, Barklund P. New genetic markers for identifying Cronartium flaccidum and Peridermium pini and examining genetic variation within and between lesions of Scots pine blister rust in Sweden. Fungal Biol 2011; 115:1303-11. [PMID: 22115449 DOI: 10.1016/j.funbio.2011.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/05/2011] [Accepted: 09/27/2011] [Indexed: 10/17/2022]
Abstract
Microsatellite markers were developed as an identification tool and for analysis of the genetic variation in the pathogens Cronartium flaccidum and Peridermium pini, causing Scots pine blister rust in Pinus spp. Six reference aeciospore samples from Finland were used to examine genetic differences between the two pathogens. Genetic variation within and between 27 lesions on Scots pines from seven locations in Sweden was also investigated. Aeciospores were collected from single aecia within the lesions. Reference samples from P. pini were homozygous for all seven microsatellite loci investigated, while the three C. flaccidum samples contained heterozygous loci. These results confirm previous studies, where homozygous aeciospores were indicated to be characteristic for P. pini. The majority of aeciospores had two nuclei in both heterozygotic and homozygotic samples. Five of the Swedish lesions contained only homozygotic aecia, while the aecia in the remaining 22 lesions were heterozygotic. All lesions with homozygotic aecia contained only one single multilocus genotype, while many of the lesions with heterozygotic aecia contained several genotypes. The latter indicates the occurrence of multiple matings within a lesion between the resident spermogonia and alien fertilizing spermatia.
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Affiliation(s)
- Berit Samils
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.
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