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Hassett K, Muria-Gonzalez MJ, Martin A, Karakaya A, Çelik Oğuz A, Bakonyi J, Knight NL, Prins R, Ellwood SR. Global Spread, Genetic Differentiation, and Selection of Barley Spot Form Net Blotch Isolates. PHYTOPATHOLOGY 2024; 114:1542-1553. [PMID: 38619562 DOI: 10.1094/phyto-11-23-0442-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Aziz Karakaya
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Arzu Çelik Oğuz
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Jószef Bakonyi
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó str. 15, 1022 Budapest, Hungary
| | - Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Renée Prins
- CenGen (Pty) Ltd., Worcester, 6850, South Africa
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Hodgson LM, Rakshit S, Lopez-Ruiz FJ, Gibberd MR, Thomas GJ, Zerihun A. Spatial Dependency in Stubble-Borne Pyrenophora teres f. teres and Influence of Sample Support Size on DNA Concentration and Fungicide Resistance Frequency. PHYTOPATHOLOGY 2024; 114:269-281. [PMID: 37505095 DOI: 10.1094/phyto-02-23-0062-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Fungicide resistance in foliar fungal pathogens is an increasing challenge to crop production. Yield impacts due to loss of fungicide efficacy may be reduced through effective surveillance and appropriate management intervention. For stubble-borne pathogens, off-season crop residues may be used to monitor fungicide resistance to inform pre-planting decisions; however, appropriate sampling strategies and support sizes for crop residues have not previously been considered. Here, we used Pyrenophora teres f. teres (Ptt) with resistance to demethylase inhibitor fungicides as a model system to assess spatial dependency and to compare the effects of different sampling strategies and support sizes on pathogen density (Ptt DNA concentration) and the frequency of fungicide resistance mutation. The results showed that sampling strategies (hand-picked versus raked) did not affect estimates of pathogen density or fungicide resistance frequency; however, sample variances were lower from raked samples. The effects of differing sample support size, as the size of the collection area (1.2, 8.6, or 60 m2), on fungicide resistance frequency were not evident (P > 0.05). However, measures of pathogen density increased with area size (P < 0.05); the 60 m2 area yielded the highest Ptt DNA concentration and produced the lowest number of pathogen-absent samples. Sample variances for pathogen density and fungicide resistance frequency were generally homogeneous between area sizes. The pattern of pathogen density was spatially independent; however, spatial dependency was identified for fungicide resistance frequency, with a range of 110 m, in one of the two fields surveyed. Collectively, the results inform designs for monitoring of fungicide resistance in stubble-borne pathogens.
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Affiliation(s)
- Leon M Hodgson
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Suman Rakshit
- Curtin Biometry and Agriculture Data Analytics, Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- School of Electrical Engineering, Computing and Mathematical Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Geoff J Thomas
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Richards JK, Li J, Koladia V, Wyatt NA, Rehman S, Brueggeman RS, Friesen TL. A Moroccan Pyrenophora teres f. teres Population Defeats Rpt5, the Broadly Effective Resistance on Barley Chromosome 6H. PHYTOPATHOLOGY 2024; 114:193-199. [PMID: 37386751 DOI: 10.1094/phyto-04-23-0117-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Net form net blotch (NFNB), caused by Pyrenophora teres f. teres, is an important barley disease. The centromeric region of barley chromosome 6H has often been associated with resistance or susceptibility to NFNB, including the broadly effective dominant resistance gene Rpt5 derived from barley line CIho 5791. We characterized a population of Moroccan P. teres f. teres isolates that had overcome Rpt5 resistance and identified quantitative trait loci (QTL) that were effective against these isolates. Eight Moroccan P. teres f. teres isolates were phenotyped on barley lines CIho 5791 and Tifang. Six isolates were virulent on CIho 5791, and two were avirulent. A CIho 5791 × Tifang recombinant inbred line (RIL) population was phenotyped with all eight isolates and confirmed the defeat of the 6H resistance locus formerly mapped as Rpt5 in barley line CI9819. A major QTL on chromosome 3H with the resistance allele derived from Tifang, as well as minor QTL, was identified and provided resistance against these isolates. F2 segregation ratios supported dominant inheritance for both the 3H and 6H resistance. Furthermore, inoculation of progeny isolates derived from a cross of P. teres f. teres isolates 0-1 (virulent on Tifang/avirulent on CIho 5791) and MorSM 40-3 (avirulent on Tifang/virulent on CIho 5791) onto the RIL and F2 populations determined that recombination between isolates can generate novel genotypes that overcome both resistance genes. Markers linked to the QTL identified in this study can be used to incorporate both resistance loci into elite barley cultivars for durable resistance.
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Affiliation(s)
- Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jinling Li
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Vaidehi Koladia
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Nathan A Wyatt
- Cereal Crops Research Unit, Edward T. Schaffer Agricultural Research Center, USDA-ARS, Fargo, ND 58102, U.S.A
| | - Sajid Rehman
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco 10010
| | - Robert S Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, U.S.A
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- Cereal Crops Research Unit, Edward T. Schaffer Agricultural Research Center, USDA-ARS, Fargo, ND 58102, U.S.A
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Hassett K, Muria-Gonzalez MJ, Turner A, McLean MS, Wallwork H, Martin A, Ellwood SR. Widespread genetic heterogeneity and genotypic grouping associated with fungicide resistance among barley spot form net blotch isolates in Australia. G3 (BETHESDA, MD.) 2023; 13:jkad076. [PMID: 37002913 PMCID: PMC10151411 DOI: 10.1093/g3journal/jkad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 04/04/2023]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a major foliar disease of barley worldwide. Knowledge of the pathogen's genetic diversity and population structure is critical for a better understanding of inherent evolutionary capacity and for the development of sustainable disease management strategies. Genome-wide, single nucleotide polymorphism data of 254 Australian isolates revealed genotypic diversity and an absence of population structure, either between states, or between fields and cultivars in different agro-ecological zones. This indicates there is little geographical isolation or cultivar directional selection and that the pathogen is highly mobile across the continent. However, two cryptic genotypic groups were found only in Western Australia, predominantly associated with genes involved in fungicide resistance. The findings in this study are discussed in the context of current cultivar resistance and the pathogen's adaptive potential.
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Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | | | - Aleesha Turner
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Mark S McLean
- Field Crops Pathology, Agriculture Victoria, Horsham, Victoria 3401, Australia
| | - Hugh Wallwork
- Cereal Pathology Laboratory, South Australian Research and Development Institute, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4350, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
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Dahanayaka BA, Snyman L, Vaghefi N, Martin A. Using a Hybrid Mapping Population to Identify Genomic Regions of Pyrenophora teres Associated With Virulence. FRONTIERS IN PLANT SCIENCE 2022; 13:925107. [PMID: 35812984 PMCID: PMC9260246 DOI: 10.3389/fpls.2022.925107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 05/26/2023]
Abstract
Net blotches caused by Pyrenophora teres are important foliar fungal diseases of barley and result in significant yield losses of up to 40%. The two types of net blotch, net-form net blotch and spot-form net blotch, are caused by P. teres f. teres (Ptt) and P. teres f. maculata (Ptm), respectively. This study is the first to use a cross between Ptt and Ptm to identify quantitative trait loci (QTL) associated with virulence and leaf symptoms. A genetic map consisting of 1,965 Diversity Arrays Technology (DArT) markers was constructed using 351 progenies of the Ptt/Ptm cross. Eight barley cultivars showing differential reactions to the parental isolates were used to phenotype the hybrid progeny isolates. Five QTL associated with virulence and four QTL associated with leaf symptoms were identified across five linkage groups. Phenotypic variation explained by these QTL ranged from 6 to 16%. Further phenotyping of selected progeny isolates on 12 more barley cultivars revealed that three progeny isolates are moderately to highly virulent across these cultivars. The results of this study suggest that accumulation of QTL in hybrid isolates can result in enhanced virulence.
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Affiliation(s)
| | - Lislé Snyman
- Department of Agriculture and Fisheries Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
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Management of Pyrenophora teres f. teres, the Causal Agent of Net Form Net Blotch of Barley, in A Two-Year Field Experiment in Central Italy. Pathogens 2022; 11:pathogens11030291. [PMID: 35335615 PMCID: PMC8954409 DOI: 10.3390/pathogens11030291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Pyrenophora teres is the causal agent of barley net blotch (NB), a disease that can be found in two different forms: net form (NFNB), caused by P. teres f. teres, and spot form (SFNB), caused by P. teres f. maculata. A two-year field experiment was carried out to evaluate the response to NB of six different barley cultivars for malt or feed/food production. In addition, the efficacy of several recently developed foliar fungicides with different modes of action (SDHI, DMI, and QoI) towards the disease was examined. After NB leaf symptom evaluation, the identification of P. teres forms was performed. Grain yield was determined, and pathogen biomass was quantified in the grain by qPCR. In the two experimental years characterized by different climatic conditions, only P. teres f. teres was detected. The tested cultivars showed different levels of NFNB susceptibility. In particular, the two-row cultivars for malt production showed the highest disease incidence. All applied fungicides exhibited a high efficacy in reducing disease symptoms on leaves and pathogen accumulation in grains. In fact, high levels of fungal biomass were detected only in the grain of the untreated malting barley cultivars. For some cultivars, grain yield was positively influenced by the application of fungicides.
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Dahanayaka BA, Vaghefi N, Knight NL, Bakonyi J, Prins R, Seress D, Snyman L, Martin A. Population Structure of Pyrenophora teres f. teres Barley Pathogens from Different Continents. PHYTOPATHOLOGY 2021; 111:2118-2129. [PMID: 33926197 DOI: 10.1094/phyto-09-20-0390-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Net form net blotch disease, caused by Pyrenophora teres f. teres, results in significant yield losses to barley industries. Up-to-date knowledge of the genetic diversity and structure of pathogen populations is critical for elucidating the disease epidemiology and unraveling pathogen survival and dispersal mechanisms. Thus, this study investigated long-distance dispersal and adaptation by analyzing the genetic structure of 250 P. teres f. teres isolates collected from Australia, Canada, Hungary, and Republic of South Africa (RSA), and historical isolates from Canada, Denmark, Japan, and Sweden. The population genetic structure detected by discriminant analysis of principal components, with the use of 5,890 Diversity Arrays Technology markers, revealed the presence of four clusters. Two of these contained isolates from all regions, and all isolates from RSA were grouped in these two. Australia and Hungary showed three clusters each. One of the Australian clusters contained only Australian isolates. One of the Hungarian clusters contained only Hungarian isolates and one Danish isolate. STRUCTURE analysis indicated that some isolates from Australia and Hungary shared recent ancestry with RSA, Canada, and historical isolates and were thus admixed. Subdivisions of the neighbor joining network indicated that isolates from distinct countries were closely related, suggesting that multiple introduction events conferred genetic heterogeneity in these countries. Through a neighbor joining analysis and amplification with form-specific DNA markers, we detected two hybrid isolates, CBS 281.31 from Japan and H-919 from Hungary, collected in 1931 and 2018, respectively. These results provide a foundation for exploring improved management of disease incursions and pathogen control through strategic deployment of resistance.
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Affiliation(s)
- Buddhika A Dahanayaka
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Noel L Knight
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - József Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Budapest, 1022, Hungary
| | - Renée Prins
- CenGen (Pty) Ltd, Worcester, 6850, South Africa
- Stellenbosch University, Department of Genetics, Matieland, Stellenbosch, 7602, South Africa
| | - Diána Seress
- Plant Protection Institute, Centre for Agricultural Research, Budapest, 1022, Hungary
| | - Lislé Snyman
- Department of Agriculture and Fisheries Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
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Backes A, Guerriero G, Ait Barka E, Jacquard C. Pyrenophora teres: Taxonomy, Morphology, Interaction With Barley, and Mode of Control. FRONTIERS IN PLANT SCIENCE 2021; 12:614951. [PMID: 33889162 PMCID: PMC8055952 DOI: 10.3389/fpls.2021.614951] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/08/2021] [Indexed: 05/27/2023]
Abstract
Net blotch, induced by the ascomycete Pyrenophora teres, has become among the most important disease of barley (Hordeum vulgare L.). Easily recognizable by brown reticulated stripes on the sensitive barley leaves, net blotch reduces the yield by up to 40% and decreases seed quality. The life cycle, the mode of dispersion and the development of the pathogen, allow a quick contamination of the host. Crop residues, seeds, and wild grass species are the inoculum sources to spread the disease. The interaction between the barley plant and the fungus is complex and involves physiological changes with the emergence of symptoms on barley and genetic changes including the modulation of different genes involved in the defense pathways. The genes of net blotch resistance have been identified and their localizations are distributed on seven barley chromosomes. Considering the importance of this disease, several management approaches have been performed to control net blotch. One of them is the use of beneficial bacteria colonizing the rhizosphere, collectively referred to as Plant Growth Promoting Rhizobacteria. Several studies have reported the protective role of these bacteria and their metabolites against potential pathogens. Based on the available data, we expose a comprehensive review of Pyrenophora teres including its morphology, interaction with the host plant and means of control.
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Affiliation(s)
- Aurélie Backes
- Unité de Recherche Résistance Induite et Bioprotection des Plantes, Université de Reims Champagne-Ardenne, Reims, France
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Hautcharage, Luxembourg
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bioprotection des Plantes, Université de Reims Champagne-Ardenne, Reims, France
| | - Cédric Jacquard
- Unité de Recherche Résistance Induite et Bioprotection des Plantes, Université de Reims Champagne-Ardenne, Reims, France
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Lelwala RV, Scott JB, Ades PK, Taylor PWJ. Population Structure of Colletotrichum tanaceti in Australian Pyrethrum Reveals High Evolutionary Potential. PHYTOPATHOLOGY 2019; 109:1779-1792. [PMID: 31179858 DOI: 10.1094/phyto-03-19-0091-r] [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] [Indexed: 06/09/2023]
Abstract
Colletotrichum tanaceti, the causal agent of anthracnose, is an emerging pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium) in Australia. A microsatellite marker library was developed to understand the spatio-genetic structure over three sampled years and across two regions where pyrethrum is cultivated in Australia. Results indicated that C. tanaceti was highly diverse with a mixed reproductive mode; comprising both sexual and clonal reproduction. Sexual reproduction of C. tanaceti was more prevalent in Tasmania than in Victoria. Little differentiation was observed among field populations likely due to isolation by colonization but most of the genetic variation was occurring within populations. C. tanaceti was likely to have had a long-distance gene and genotype flow among distant populations within a state and between states. Anthropogenic transmission of propagules and wind dispersal of ascospores are the most probable mechanisms of long-distance dispersal of C. tanaceti. Evaluation of putative population histories suggested that C. tanaceti most likely originated in Tasmania and expanded from an unidentified host onto pyrethrum. Victoria was later invaded by the Tasmanian population. With the mixed mode of reproduction and possible long-distance gene flow, C. tanaceti is likely to have a high evolutionary potential and thereby has ability to adapt to management practices in the future.
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Affiliation(s)
- Ruvini V Lelwala
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
| | - Jason B Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia 7320
| | - Peter K Ades
- School of Ecosystem and Forest Sciences, University of Melbourne, Victoria, Australia 3010
| | - Paul W J Taylor
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
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Linde CC, Smith LM. Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass. BMC Evol Biol 2019; 19:139. [PMID: 31286867 PMCID: PMC6615293 DOI: 10.1186/s12862-019-1446-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 05/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background Pathogens evolve in an arms race, frequently evolving virulence that defeats resistance genes in their hosts. Infection of multiple hosts may accelerate this virulence evolution. Theory predicts that host diversity affects pathogen diversity, with more diverse hosts expected to harbour more diverse pathogens that reproduce sexually. We tested this hypothesis by comparing the microsatellite (SSR) genetic diversity of the barley leaf pathogen Pyrenophora teres f. teres (Ptt) from barley (monoculture) and barley grass (outbreeding). We also aim to investigate host specificity and attempt to track virulence on two barley cultivars, Maritime and Keel. Results Genetic diversity in barley Ptt populations was higher than in populations from barley grass. Barley Ptt populations also had higher linkage disequilibrium levels, indicating less frequent sexual reproduction, consistent with the Red Queen hypothesis theory that genetically diverse hosts should select for higher levels of sexual reproduction of the pathogen. SSR analyses indicate that host-associated Ptt populations do not share genotypes and have independent evolutionary histories. Pathogenicity studies showed host specificity as host-associated Ptt isolates could not cross-infect hosts. Minimum spanning network analyses indicated two major clusters of barley Ptt. One cluster represents Maritime virulent and isolates from Western Australia (WA). Low PhiPt population differentiation between WA populations and those from Maritime and Keel, indicated a WA origin of the Maritime and Keel virulences. The main minimum spanning network cluster is represented by a panmictic population structure, represented by isolates from all over Australia. Conclusions Although barley Ptt populations are more diverse than barley grass Ptt populations, this may be a result of the size and number of founder Ptt populations to Australia, with larger and more barley Ptt populations introduced. More frequent sexual reproduction of Ptt on barley grass support the Red Queen Hypothesis and suggest evolutionary potential of pathogens on diverse hosts are high. Extensive gene flow of Ptt between regions in Australia is suggested to maintain a panmictic population structure, with human-mediated dispersal aiding in virulence evolution of Ptt on barley. Electronic supplementary material The online version of this article (10.1186/s12862-019-1446-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Celeste C Linde
- Division of Ecology and Evolution, Research School of Biology, ANU College of Science, The Australian National University, RN Robertson Building, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia.
| | - Leon M Smith
- Division of Ecology and Evolution, Research School of Biology, ANU College of Science, The Australian National University, RN Robertson Building, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
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Pearce TL, Scott JB, Pilkington SJ, Pethybridge SJ, Hay FS. Evidence for Sexual Recombination in Didymella tanaceti Populations, and Their Evolution Over Spring Production in Australian Pyrethrum Fields. PHYTOPATHOLOGY 2019; 109:155-168. [PMID: 29989847 DOI: 10.1094/phyto-08-17-0280-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tan spot, caused by Didymella tanaceti, is one of the most important foliar diseases affecting pyrethrum in Tasmania, Australia. Population dynamics, including mating-type ratios and genetic diversity of D. tanaceti, was characterized within four geographically separated fields in both late winter and spring 2012. A set of 10 microsatellite markers was developed and used to genotype 774 D. tanaceti isolates. Isolates were genotypically diverse, with 123 multilocus genotypes (MLG) identified across the four fields. Fifty-eight MLG contained single isolates and Psex analysis estimated that, within many of the recurrent MLG, there were multiple clonal lineages derived from recombination. Isolates of both mating types were at a 1:1 ratio following clone correction in each field at each sampling period, which was suggestive of sexual recombination. No evidence of genetic divergence of isolates of each mating type was identified, indicating admixture within the population. Linkage equilibrium in two of the four field populations sampled in late winter could not be discounted following clone correction. Evaluation of temporal changes in gene and genotypic diversity identified that they were both similar for the two sampling periods despite an increased D. tanaceti isolation frequency in spring. Genetic differentiation was similar in populations sampled between the two sampling periods within fields or between fields. These results indicated that sexual reproduction may have contributed to tan spot epidemics within Australian pyrethrum fields and has contributed to a genetically diverse D. tanaceti population.
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Affiliation(s)
- Tamieka L Pearce
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Jason B Scott
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Stacey J Pilkington
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Frank S Hay
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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Syme RA, Martin A, Wyatt NA, Lawrence JA, Muria-Gonzalez MJ, Friesen TL, Ellwood SR. Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host-Pathogen Genetic Interactions. Front Genet 2018; 9:130. [PMID: 29720997 PMCID: PMC5915480 DOI: 10.3389/fgene.2018.00130] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range of host-pathogen genetic interactions compared to other Pyrenophora spp., a property which associates better with genome size than pathogen lifestyle. The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. Tad-1 was only detectable as vestigial fragments in PTM and, within the forms, differences in genome sizes and the presence and absence of several TE families indicated recent lineage invasions. Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. Instances of gene interruption by transposons resulting in pseudogenization were detected in PTT. In addition, both forms have a large complement of secondary metabolite gene clusters indicating significant capacity to produce an array of different molecules. This study provides genomic resources for functional genetics to help dissect factors underlying the host-pathogen interactions.
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Affiliation(s)
- Robert A. Syme
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Nathan A. Wyatt
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Julie A. Lawrence
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Mariano J. Muria-Gonzalez
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Simon R. Ellwood
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
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Poudel B, Ellwood SR, Testa AC, McLean M, Sutherland MW, Martin A. Rare Pyrenophora teres Hybridization Events Revealed by Development of Sequence-Specific PCR Markers. PHYTOPATHOLOGY 2017; 107:878-884. [PMID: 28409525 DOI: 10.1094/phyto-11-16-0396-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pyrenophora teres f. teres and P. teres f. maculata cause net form and spot form, respectively, of net blotch on barley (Hordeum vulgare). The two forms reproduce sexually, producing hybrids with genetic and pathogenic variability. Phenotypic identification of hybrids is challenging because lesions induced by hybrids on host plants resemble lesions induced by either P. teres f. teres or P. teres f. maculata. In this study, 12 sequence-specific polymerase chain reaction markers were developed based on expressed regions spread across the genome. The primers were validated using 210 P. teres isolates, 2 putative field hybrids (WAC10721 and SNB172), 50 laboratory-produced hybrids, and 7 isolates collected from barley grass (H. leporinum). The sequence-specific markers confirmed isolate WAC10721 as a hybrid. Only four P. teres f. teres markers amplified on DNA of barley grass isolates. Amplified fragment length polymorphism markers suggested that P. teres barley grass isolates are genetically different from P. teres barley isolates and that the second putative hybrid (SNB172) is a barley grass isolate. We developed a suite of markers which clearly distinguish the two forms of P. teres and enable unambiguous identification of hybrids.
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Affiliation(s)
- Barsha Poudel
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
| | - Simon R Ellwood
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
| | - Alison C Testa
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
| | - Mark McLean
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
| | - Mark W Sutherland
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
| | - Anke Martin
- First, fifth, and sixth authors: University of Southern Queensland Centre for Crop Health, Toowoomba, Queensland, 4350, Australia; second and third authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley Western Australia, 6102, Australia; and fourth author: Agriculture Victoria, Horsham, Victoria, 3401, Australia
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Mironenko NV, Baranova OA, Kovalenko NM, Mikhailova LA, Rosseva LP. Genetic structure of the Russian populations of Pyrenophora tritici-repentis, determined by using microsatellite markers. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416080093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ismail IA, Able AJ. Secretome analysis of virulent Pyrenophora teres f. teres isolates. Proteomics 2016; 16:2625-2636. [PMID: 27402336 DOI: 10.1002/pmic.201500498] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 06/24/2016] [Accepted: 07/07/2016] [Indexed: 11/11/2022]
Abstract
Pyrenophora teres f. teres (Ptt) causes net form net blotch disease of barley, partially by producing necrosis-inducing proteins. The protein profiles of the culture filtrates of 28 virulent isolates were compared by a combination of 2DE and 1D-PAGE with 105 spots and 51 bands chosen for analysis by liquid chromatography electrospray ionization tandem mass spectrometry. A total of 259 individual proteins were identified with 63 of these proteins being common to the selected virulent isolates. Ptt secretes a broad spectrum of proteins including cell wall degrading enzymes; virulence factors and effectors; proteins associated with fungal pathogenesis and development; and proteins related to oxidation-reduction processes. Potential virulence factors and effectors identified included proteins with glucosidase activity, ricin B and concanavalin A-like lectins, glucanases, spherulin, cutinase, pectin lyase, leucine-rich repeat protein, and ceratoplatanin. Small proteins with unknown function but cysteine-rich, common to effectors, were also identified. Differences in the secretion profile of the Ptt isolates have also provided important insight into the different mechanisms contributing to virulence and the development of net form net blotch symptoms.
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Affiliation(s)
- Ismail A Ismail
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia.
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Genetic structure of Pyrenophora teres net and spot populations as revealed by microsatellite analysis. Fungal Biol 2013; 118:180-92. [PMID: 24528640 DOI: 10.1016/j.funbio.2013.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/08/2013] [Accepted: 11/18/2013] [Indexed: 11/22/2022]
Abstract
The population structure of the fungal pathogen Pyrenophora teres, collected mainly from different regions of the Czech and Slovak Republics, was examined using a microsatellite analyses (SSR). Among 305 P. teres f. teres (PTT) and 82 P. teres f. maculata (PTM) isolates that were collected, the overall gene diversity was similar (ĥ = 0.12 and ĥ = 0.13, respectively). A high level of genetic differentiation (FST = 0.46; P < 0.001) indicated the existence of population structure. Nine clusters that were found using a Bayesian approach represent the genetic structure of the studied P. teres populations. Two clusters consisted of PTM populations; PTT populations formed another seven clusters. An exact test of population differentiation confirmed the results that were generated by Structure. There was no difference between naturally infected populations over time, and genetic distance did not correlate with geographical distance. The facts that all individuals had unique multilocus genotypes and that the hypothesis of random mating could not be rejected in several populations or subpopulations serve as evidence that a mixed mating system plays a role in the P. teres life cycle. Despite the fact that the genetic differentiation value between PTT and PTM (FST = 0.30; P < 0.001) is lower than it is between the populations within each form (FST = 0.40 (PTT); FST = 0.35 (PTM); P < 0.001) and that individuals with mixed PTT and PTM genomes were found, the two forms of P. teres form genetically separate populations. Therefore, it can be assumed that these populations have most likely undergone speciation.
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Brewer MT, Frenkel O, Milgroom MG. Linkage disequilibrium and spatial aggregation of genotypes in sexually reproducing populations of Erysiphe necator. PHYTOPATHOLOGY 2012; 102:997-1005. [PMID: 22755546 DOI: 10.1094/phyto-11-11-0321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Random mating and recombination in heterothallic ascomycetes should result in high genotypic diversity, 1:1 mating-type ratios, and random associations of alleles, or linkage equilibrium, at different loci. To test for random mating in populations of the grape powdery mildew fungus Erysiphe necator, we sampled isolates from vineyards of Vitis vinifera in Burdett, NY (NY09) and Winchester, VA (VA09) at the end of the epidemic in fall 2009. We also sampled isolates from the same Winchester, VA vineyard in spring 2010 at the onset of the next epidemic. Isolates were genotyped for mating type and 11 microsatellite markers. In the spring sample, which originated from ascospore infections, nearly every isolate had a unique genotype. In contrast, fall populations were less diverse. In all, 9 of 45 total genotypes in VA09 were represented by two or more isolates; 3 of 40 total genotypes in NY09 were represented by two or more isolates, with 1 genotype represented by 20 isolates. After clone correction, mating-type ratios in the three populations did not deviate from 1:1. However, even with clone correction, we detected significant linkage disequilibrium (LD) in all populations. Mantel tests detected positive correlations between genetic and physical distances within vineyards. Spatial autocorrelation showed aggregations up to 42 and 3 m in VA09 and NY09, respectively. Spatial autocorrelation most likely results from short dispersal distances. Overall, these results suggest that spatial genetic aggregation and clonal genotypes that arise during the asexual phase of the epidemic contribute to persistent LD even though populations undergo sexual reproduction annually.
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Affiliation(s)
- Marin Talbot Brewer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
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Ellwood SR, Syme RA, Moffat CS, Oliver RP. Evolution of three Pyrenophora cereal pathogens: recent divergence, speciation and evolution of non-coding DNA. Fungal Genet Biol 2012; 49:825-9. [PMID: 22850609 DOI: 10.1016/j.fgb.2012.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/05/2012] [Accepted: 07/19/2012] [Indexed: 12/22/2022]
Abstract
Three of the most important fungal pathogens of cereals are Pyrenophora tritici-repentis, the cause of tan spot on wheat, and Pyrenophora teres f. teres and Pyrenophora teres f. maculata, the cause of spot form and net form of net blotch on barley, respectively. Orthologous intergenic regions were used to examine the genetic relationships and divergence times between these pathogens. Mean divergence times were calculated at 519 kya (±30) between P. teresf. teres and P. teresf. maculata, while P. tritici-repentis diverged from both Pyrenophora teresforms 8.04 Mya (±138 ky). Individual intergenic regions showed a consistent pattern of co-divergence of the P. teresforms from P. tritici-repentis, with the pattern supported by phylogenetic analysis of conserved genes. Differences in calculated divergence times between individual intergenic regions suggested that they are not entirely under neutral selection, a phenomenon shared with higher Eukaryotes. P. tritici-repentis regions varied in divergence time approximately 5-12 Mya from the P. teres lineage, compared to the separation of wheat and barley some 12 Mya, while the P. teresf. teres and P. teresf. maculata intergenic region divergences correspond to the middle Pleistocene. The data suggest there is no correlation between the divergence of these pathogens the domestication of wheat and barley, and show P. teresf. teres and P. teresf. maculata are closely related but autonomous. The results are discussed in the context of speciation and the evolution of intergenic regions.
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Affiliation(s)
- Simon R Ellwood
- Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia 6102, Australia.
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Abstract
Comparing to natural ecosystems, the evolution of plant pathogens in agricultural ecosystems is generally faster due to high-density monocultures, large-scale application of agrochemicals, and international trade in agricultural products. Knowledge of the population genetics and evolutionary biology of plant pathogens is necessary to understand disease epidemiology, effectively breed and use resistant cultivars, and control plant diseases. In this article, we outlined the aims of population genetic studies in plant pathogens, discuss contributions of five evolutionary forces (i.e., mutation, gene flow, recombination, random genetic drift, and natural selection) to origin, maintenance, and distribution of genetic variation in time and space, and gave an overview of current research status in this field.
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Affiliation(s)
- Wen Zhu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China.
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