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Mainello-Land A, Saville AC, Acharya J, Ristaino J. Loop-Mediated Isothermal Amplification Detection of Phytophthora kernoviae, P. ramorum, and the P. ramorum NA1 Lineage on a Microfluidic Chip and Smartphone Platform. PHYTOPATHOLOGY 2025; 115:192-203. [PMID: 39434003 DOI: 10.1094/phyto-02-24-0055-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: 10/23/2024]
Abstract
Rapid, field-deployable assays such as loop-mediated isothermal amplification (LAMP) are critical for detecting nursery and forest pathogens such as Phytophthora ramorum and P. kernoviae to prevent pathogen spread. We developed and validated four LAMP assays for genus-level detection of Phytophthora spp., species-level detection of P. kernoviae and P. ramorum, and lineage-level detection of the P. ramorum NA1 lineage. The cross-reactivity of the two species-specific LAMP assays was evaluated using a set of 18 Phytophthora spp. known to infect nursery crop hosts. The correct target species were detected by the species-level LAMP assays. The Phytophthora spp. LAMP assay was evaluated against 27 Phytophthora spp. and other bacterial and fungal pathogens and reacted with all the Phytophthora spp. evaluated but no other bacterial or fungal species. The limit of detection (LOD) of the P. kernoviae LAMP was 100 fg/µl, and the LOD of the P. ramorum LAMP assay was 1 pg/µl of DNA. The NA1 LAMP assay was tested against the NA1, NA2, EU1, and EU2 lineages of P. ramorum and was lineage-specific but had a higher LOD (100 pg/µl) than the species-specific LAMP assays. Both P. ramorum and P. kernoviae LAMP assays were highly precise (>0.94) in detecting the respective pathogens in symptomatic rhododendron leaves and co-inoculation experiments. The four LAMP assays were run in tandem on a microfluidic chip and smartphone platform and can be used in the field to detect and monitor spread of these regulatory Phytophthora spp. in forest and/or nursery settings.
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Affiliation(s)
- Amanda Mainello-Land
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Amanda C Saville
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Jyotsna Acharya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
| | - Jean Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
- Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC 27695, U.S.A
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Gomes M, Ralph TJ, Humphries MS, Graves BP, Kobayashi T, Gore DB. Waterborne contaminants in high intensity agriculture and plant production: A review of on-site and downstream impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:178084. [PMID: 39674148 DOI: 10.1016/j.scitotenv.2024.178084] [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: 09/10/2024] [Revised: 12/02/2024] [Accepted: 12/10/2024] [Indexed: 12/16/2024]
Abstract
Waterborne contaminants pose a significant risk to water quality and plant health in agricultural systems. This is particularly the case for relatively small-scale but intensive agricultural operations such as plant production nurseries that often rely on recycled irrigation water. The increasing global demand for plants requires improved water quality and more certainty around water availability, which may be difficult to predict and deliver due to variable and changing climate regimes. Production nurseries are moving to adopt best management practices that recycle water; however, the risks associated with waterborne contaminants of various types, including nutrients, pesticides, plant pathogens, micro-plastics, and toxic metals, are not well understood. We review and synthesise the physical and biogeochemical factors that contribute to waterborne contaminant risk, and the main types of contaminants that are likely to require management, at plant production nurseries. Catchment characteristics (i.e., topography, land use), hydroclimatic factors (i.e., storms, floods, droughts), and landscape hydrological and sediment connectivity influence surface runoff, sediment transport, and associated contaminant transfer and storage. High hydrological connectivity can increase the risk of contaminant transport from the surrounding landscape to nurseries, with potential negative impacts to water quality in reservoirs and in turn plant health. High connectivity may also increase the risk of contaminants (e.g., sediment, pesticides, and phytopathogens) being transferred from nursery farms into downstream waterways, with consequences for aquatic ecosystems. Like all intensive agricultural operations, nurseries need to consider sources of irrigation water, water treatment and management strategies, and catchment and hydroclimatic factors, to mitigate the spread of contaminants and reduce their impacts on both plant production and the surrounding environment. Further research is needed to quantify contaminant loads and transfer pathways in these agricultural systems, and to better understand the threshold levels of contaminants that adversely affect plant health and which may result in devastating economic losses.
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Affiliation(s)
- Megan Gomes
- School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa; School of Natural Sciences, Macquarie University, NSW, Australia.
| | - Timothy J Ralph
- School of Natural Sciences, Macquarie University, NSW, Australia
| | - Marc S Humphries
- School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - Bradley P Graves
- School of Natural Sciences, Macquarie University, NSW, Australia
| | - Tsuyoshi Kobayashi
- Science and Insights Division, Department of Climate Change, Energy, the Environment and Water, NSW, Australia
| | - Damian B Gore
- School of Natural Sciences, Macquarie University, NSW, Australia
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Marin MV, Ratti MF, Peres NA, Goss EM. New Genotypes of Phytophthora nicotianae Found on Strawberry in Florida. PHYTOPATHOLOGY 2024; 114:743-751. [PMID: 37942874 DOI: 10.1094/phyto-05-23-0175-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: 11/10/2023]
Abstract
Phytophthora cactorum is the most common causal agent of Phytophthora crown rot and leather rot of strawberry, but P. nicotianae is also responsible for the disease in Florida. Studies of P. nicotianae populations have suggested that different groups of genotypes are associated with different hosts; however, it is not yet clear how many lineages exist globally and how they are related to different production systems. The aim of this study was to determine the genetic relationships of P. nicotianae isolates from Florida strawberry with genotypes reported from other hosts, quantify the genetic variation on strawberry, and test for an association with nursery source. A total of 49 isolates of P. nicotianae were collected from strawberry plants originating from multiple nursery sources during six seasons of commercial fruit production in Florida. Microsatellite genotyping identified 28 multilocus genotypes on strawberry that were distinct among 208 isolates originating from various hosts and locations. Based on STRUCTURE analysis, two genetic groups were identified: one consisting of isolates from strawberry, and the other comprising samples from different hosts. Multilocus genotypes were shared among nursery sources, and populations defined by nursery were not differentiated. Both mating types were found among the isolates from North Carolina- and California-origin plants and in most strawberry seasons; however, a predominance of A1 was observed, and regular sexual reproduction was not supported by the data. This study reveals a unique genetic population of P. nicotianae associated with strawberry and emphasizes the vital role of nursery monitoring in mitigating disease spread.
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Affiliation(s)
- Marcus V Marin
- Department of Plant Pathology, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
| | - Maria F Ratti
- Escuela Superior Politecnica del Litoral, Guayaquil, Guayas, República del Ecuador
| | - Natalia A Peres
- Department of Plant Pathology, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
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Søndreli KL, Tabima JF, LeBoldus JM. Rapid New Diagnostic LAMP (Loop-Mediated Isothermal Amplification) Assays to Distinguish Among the Four Lineages of Phytophthora ramorum. PLANT DISEASE 2023; 107:3553-3559. [PMID: 37194212 DOI: 10.1094/pdis-08-22-1965-re] [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: 05/18/2023]
Abstract
Sudden oak death (SOD) is caused by Phytophthora ramorum, an invasive oomycete pathogen. This pathogen is of major regulatory concern for nurseries, horticulture, and forestry in the United States and around the world. Three of the 12 identified lineages of P. ramorum currently occur in the United States (NA1, NA2, and EU1) affecting wildland forests and nurseries. Rapid identification and lineage determination is essential to accelerate management decisions, detect introductions of new lineages, and control the spread of SOD. The objective of this study was to develop and validate diagnostic tools to rapidly identify P. ramorum and distinguish among the four common lineages of the pathogen and to accelarate management decision making. The loop-mediated isothermal amplification (LAMP) assays developed here are species specific with no cross reaction to common Phytophthora species found in Oregon, California, and Washington. The lineage-specific assays unambiguously distinguish among the four common clonal lineages. These assays are sensitive and able to detect P. ramorum DNA ranging in concentration from 30 to 0.03 ng/μl depending on the assay. These assays work effectively on a variety of sample types including plant tissue, cultures, and DNA. They have been integrated into the SOD diagnostic process in the forest pathology lab at Oregon State University. To date, 190 samples have been correctly identified from over 200 field samples tested for lineage determination. The development of these assays will help managers in forestry and horticulture identify and rapidly respond to new outbreaks of P. ramorum.
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Affiliation(s)
- Kelsey L Søndreli
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Javier F Tabima
- Department of Biology, Clark University, The Lasry Center for Bioscience, Worcester, MA 01610
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331
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Lee SH, Nam B, Lee DJ, Choi YJ. Morphology, Molecular Phylogeny, and Fungicide Sensitivity of Phytophthora nagaii and P. tentaculata in Korea. MYCOBIOLOGY 2023; 51:333-342. [PMID: 37929005 PMCID: PMC10621251 DOI: 10.1080/12298093.2023.2265579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023]
Abstract
Phytophthora species, classified under Oomycota, cause significant damage to various crops and trees. The present study introduced Phytophthora species, P. nagaii and P. tentaculata, new to Korea, which pose notable risks to their respective host plants. Our research provided a comprehensive description of these species taking into account their cultural features, morphological characteristics, and molecular phylogenetic analysis using the internal transcribed spacer rDNA region and cytochrome c oxidase subunit mtDNA genes (cox1 and cox2) sequences. In addition, this study first evaluated the sensitivity of P. nagaii and P. tentaculata to five anti-oomycete fungicides, finding both species most responsive to picarbutrazox and P. tentaculata resistant to fluazinam. The data can guide targeted treatment strategies and offer insights into effective control methods. The findings expand our understanding of the diversity, distribution, and management of Phytophthora species in Korea.
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Affiliation(s)
- Seung Hyun Lee
- Department of Biological Science, Kunsan National University, Gunsan, South Korea
| | - Bora Nam
- Department of Biological Science, Kunsan National University, Gunsan, South Korea
- Center for Convergent Agrobioengineering, Kunsan National University, Gunsan, South Korea
| | - Dong Jae Lee
- Department of Biological Science, Kunsan National University, Gunsan, South Korea
| | - Young-Joon Choi
- Department of Biological Science, Kunsan National University, Gunsan, South Korea
- Center for Convergent Agrobioengineering, Kunsan National University, Gunsan, South Korea
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Bourret TB, Fajardo SN, Frankel SJ, Rizzo DM. Cataloging Phytophthora Species of Agriculture, Forests, Horticulture, and Restoration Outplantings in California, U.S.A.: A Sequence-Based Meta-Analysis. PLANT DISEASE 2023; 107:67-75. [PMID: 35724315 DOI: 10.1094/pdis-01-22-0187-re] [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: 06/15/2023]
Abstract
California contains a diverse flora, and knowledge of the pathogens that threaten those plants is essential to managing their long-term health. To better understand threats to California plant health, a meta-analysis of Phytophthora detections within the state was conducted using publicly available sequences as a primary source of data rather than published records. Accessions of internal transcribed spacer (ITS) ribosomal DNA were cataloged from 800 Californian Phytophthora isolates, analyzed, and determined to correspond to 80 taxa, including several phylogenetically distinct provisional species. A number of Phytophthora taxa not previously reported from California were identified, including 20 described species. Pathways of introduction and spread were analyzed by categorizing isolates' origins, grouped by land-use: (i) agriculture, (ii) forests and other natural ecosystems, (iii) horticulture and nurseries, or (iv) restoration outplantings. The pooled Phytophthora metacommunities of the restoration outplantings and horticulture land-use categories were the most similar, whereas the communities pooled from forests and agriculture were least similar. Phytophthora cactorum, P. pini, P. pseudocryptogea, and P. syringae were identified in all four land-use categories, while 13 species were found in three. P. gonapodyides was the most common species by number of ITS accessions and exhibited the greatest diversity of ITS haplotypes. P. cactorum, P. ramorum, and P. nicotianae were associated with the greatest number of host genera. In this analysis, the Phytophthora spp. most prevalent in California differ from those compiled from the scientific literature.
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Affiliation(s)
- Tyler B Bourret
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
| | - Sebastian N Fajardo
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
| | - Susan J Frankel
- Pacific Southwest Research Station, United States Department of Agriculture Forest Service, Albany, CA 94710
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
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LeBoldus JM, Navarro SM, Kline N, Ritokova G, Grünwald NJ. Repeated Emergence of Sudden Oak Death in Oregon: Chronology, Impact, and Management. PLANT DISEASE 2022; 106:3013-3021. [PMID: 35486603 DOI: 10.1094/pdis-02-22-0294-fe] [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: 06/14/2023]
Abstract
It has been two decades since the first detection of the sudden oak death pathogen Phytophthora ramorum in Oregon forests. Although the epidemic was managed since its first discovery in 2001, at least three invasions of three separate variants (clonal lineages), NA1, EU1, and NA2, are documented to have occurred to date. Control of this epidemic has cost over US$32 million from 2001 to 2020. This is dwarfed by the predicted cost of the closure to the Coos Bay export terminal, estimated at $58 million per year, if the epidemic was allowed to spread unchecked. Management efforts in Oregon have reduced inoculum and limited the spread of the pathogen. An outreach and citizen scientist program has been piloted to help in early detection efforts and search for disease-resistant tanoak. This feature article documents the repeated emergence, impact, costs, and lessons learned from managing this devastating invasive pathogen.
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Affiliation(s)
- Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
- Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR
| | | | - Norma Kline
- Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR
| | | | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR
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Peterson EK, Grünwald NJ, Parke JL. Risk of Epidemic Development in Nurseries from Soil Inoculum of Phytophthora ramorum. PHYTOPATHOLOGY 2022; 112:1046-1054. [PMID: 34664977 DOI: 10.1094/phyto-06-21-0245-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: 06/13/2023]
Abstract
Soilborne inoculum arising from buried, infested leaf debris may contribute to the persistence of Phytophthora ramorum at recurrently positive nurseries. To initiate new epidemics, inoculum must not only survive but also produce sporangia during times conducive to infection at the soil surface. To assess this risk, we performed two year-long experiments in a soil plot at the National Ornamentals Research Site at Dominican University of California. Inoculated rhododendron leaf disks were buried at a depth of 5 or 15 cm in the early summer of 2014 or 2015. Inoculum was baited at the soil surface with noninfested leaf disks (2014 only) and then retrieved to assess pathogen viability and sporulation capacity every 5 weeks. Two 14-week-long trials were conducted in 2016. We were able to consistently culture P. ramorum over all time periods. Soil incubation rapidly reduced the capacity of inoculum to sporulate, especially at 5 cm; however, sporulation capacity increased with the onset of seasonally cooler temperatures. P. ramorum was baited most frequently between November and January, especially from inoculum buried at 5 cm 1 day before the baiting period; in January we also baited P. ramorum from inoculum buried at 15 cm the previous June. We validate prior observations that P. ramorum poses a greater risk after exposure to cooler temperatures and provide evidence that infested leaf debris plays a role in the perpetuation of P. ramorum in nurseries. This work provides novel insights into the survival and epidemic behavior of P. ramorum in nursery soils.
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Affiliation(s)
- Ebba K Peterson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97331
| | - Jennifer L Parke
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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Van der Heyden H, Dutilleul P, Duceppe M, Bilodeau GJ, Charron J, Carisse O. Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada. MOLECULAR PLANT PATHOLOGY 2022; 23:339-354. [PMID: 34921486 PMCID: PMC8828460 DOI: 10.1111/mpp.13158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/19/2023]
Abstract
Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec-Les Jardins de Napierville-to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.
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Affiliation(s)
- Hervé Van der Heyden
- Cie de Recherche PhytodataSherringtonQuébecCanada
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | - Pierre Dutilleul
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | | | | | | | - Odile Carisse
- Agriculture and Agri‐Food CanadaSt‐Jean‐sur‐RichelieuQuébecCanada
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Guo Y, Sakalidis ML, Torres-Londono GA, Hausbeck MK. Population Structure of a Worldwide Phytophthora palmivora Collection Suggests Lack of Host Specificity and Reduced Genetic Diversity in South America and the Caribbean. PLANT DISEASE 2021; 105:4031-4041. [PMID: 33983798 DOI: 10.1094/pdis-05-20-1055-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora palmivora (Butler) is a highly destructive plant pathogen that infects tropical hosts worldwide, many of which are economically important crops. Despite the broad host range and wide distribution, the pathogen has displayed a considerable amount of variation in morphological characters, including virulence. However, the genetic variability at a global level, which is critical to understand the center of origin and the potential pathway(s) of introduction, was unclear. Here, we mapped the genetic variation of P. palmivora using isolates representing four regions, 15 countries, and 14 host species. We designed a large set of simple sequence repeat markers from the P. palmivora genome and picked 17 selectively neutral markers to screen 98 P. palmivora isolates. We found that P. palmivora populations from our collection generally did not cluster according to host; rather, some isolates from North America were generally distinct from all other populations. Isolates from South America and the Caribbean clustered and appeared to share ancestry with isolates from Asia. Populations from North America and Asia were the most genetically diverse, while the South American and Caribbean populations exhibited similar reduced genetic diversity. The isolates collected in various plantations in Colombia did not show host or geographic specificity. Our study brought a further understanding of this important plant pathogen, although the determination for hypothesized source of origin, spread, and evolution would need further sampling. The genomic resources developed in this study would facilitate further studies on P. palmivora diagnostics and management.
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Affiliation(s)
- Yufang Guo
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Monique L Sakalidis
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
- Department of Forestry, Michigan State University, East Lansing, MI 48824
| | | | - Mary K Hausbeck
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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Shakya SK, Grünwald NJ, Fieland VJ, Knaus BJ, Weiland JE, Maia C, Drenth A, Guest DI, Liew ECY, Crane C, Chang TT, Fu CH, Minh Chi N, Quang Thu P, Scanu B, von Stowasser ES, Durán Á, Horta Jung M, Jung T. Phylogeography of the wide-host range panglobal plant pathogen Phytophthora cinnamomi. Mol Ecol 2021; 30:5164-5178. [PMID: 34398981 DOI: 10.1111/mec.16109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/09/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022]
Abstract
Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi. P. cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a phylogeographic analysis of populations of this pathogen sampled in Asia, Australia, Europe, southern and northern Africa, South America, and North America. Based on genotyping-by-sequencing, we observed the highest genotypic diversity in Taiwan and Vietnam, followed by Australia and South Africa. Mating type ratios were in equal proportions in Asia as expected for a sexual population. Simulations based on the index of association suggest a partially sexual, semi-clonal mode of reproduction for the Taiwanese and Vietnamese populations while populations outside of Asia are clonal. Ancestral area reconstruction provides new evidence supporting Taiwan as the ancestral area, given our sample, indicating that this region might be near or at the centre of origin for this pathogen as speculated previously. The Australian and South African populations appear to be a secondary centre of diversity following migration from Taiwan or Vietnam. Our work also identified two panglobal, clonal lineages PcG1-A2 and PcG2-A2 of A2 mating type found on all continents. Further surveys of natural forests across Southeast Asia are needed to definitively locate the actual centre of origin of this important plant pathogen.
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Affiliation(s)
- Shankar K Shakya
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, Oregon, USA
| | - Valerie J Fieland
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Brian J Knaus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jerry E Weiland
- Horticultural Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, Oregon, USA
| | - Cristiana Maia
- Centre of Marine Sciences (CCMAR), Faculty of Sciences and Technology, University of Algarve, Faro, Portugal
| | - André Drenth
- Centre for Horticultural Science, The University of Queensland, Ecosciences Precinct, Brisbane, Queensland, Australia
| | - David I Guest
- Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Edward C Y Liew
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Colin Crane
- Vegetation Health Service, Kensington, Washington, Australia
| | - Tun-Tschu Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Chuen-Hsu Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Nguyen Minh Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
| | - Pham Quang Thu
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
| | - Bruno Scanu
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Eugenio Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Álvaro Durán
- Bioforest S.A., Casilla 70-C, Concepción, Chile.,Research and Development, Asia Pacific Resources International Limited, Pangkalan Kerinci, Indonesia
| | - Marilia Horta Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Mendel University in Brno, Brno, Czech Republic
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Mendel University in Brno, Brno, Czech Republic
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12
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Carleson NC, Daniels HA, Reeser PW, Kanaskie A, Navarro SM, LeBoldus JM, Grünwald NJ. Novel Introductions and Epidemic Dynamics of the Sudden Oak Death Pathogen Phytophthora ramorum in Oregon Forests. PHYTOPATHOLOGY 2021; 111:731-740. [PMID: 33021878 DOI: 10.1094/phyto-05-20-0164-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sudden oak death caused by Phytophthora ramorum has been actively managed in Oregon since the early 2000s. To date, this epidemic has been driven mostly by the NA1 clonal lineage of P. ramorum, but an outbreak of the EU1 lineage has recently emerged. Here, we contrast the population dynamics of the NA1 outbreak first reported in 2001 to the outbreak of the EU1 lineage first detected in 2015. We performed tests to determine whether any of the lineages were introduced more than once. Infested regions of the forest were sampled between 2013 and 2018 (n = 903), and strains were genotyped at 15 microsatellite loci. Most genotypes observed were transient, with 272 of 358 unique genotypes emerging during one year and disappearing the next year. The diversity of EU1 was very low and isolates were spatially clustered (less than 8 km apart), suggesting a single EU1 introduction. Some forest isolates are genetically similar to isolates collected from a local nursery in 2012, suggesting the introduction of EU1 from this nursery or simultaneous introduction to both the nursery and latently into the forest. In contrast, the older NA1 populations were more polymorphic and spread more than 30 km2. A principal component analysis supported two to four independent NA1 introductions. The NA1 and EU1 epidemics infest the same area but show disparate demographics because of the initial introductions of the lineages spaced 10 years apart. Comparing these epidemics provides novel insight regarding patterns of emergence of clonal pathogens in forest ecosystems.
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Affiliation(s)
- Nicholas C Carleson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - Hazel A Daniels
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - Paul W Reeser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | | | | | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
- Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR
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LeBlanc N, Cubeta MA, Crouch JA. Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood. PHYTOPATHOLOGY 2021; 111:184-193. [PMID: 33048629 DOI: 10.1094/phyto-06-20-0219-fi] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species Calonectria pseudonaviculata has remained genetically isolated from its European-limited sister species C. henricotiae, while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 C. pseudonaviculata isolates from four continents and 1,017 SNPs in 13 C. henricotiae isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in C. pseudonaviculata identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two C. pseudonaviculata genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation.
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Affiliation(s)
- Nicholas LeBlanc
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
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14
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Rasmussen DA, Grünwald NJ. Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY 2021; 111:68-77. [PMID: 33021879 DOI: 10.1094/phyto-07-20-0319-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.
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Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR
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15
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Widmer TL, McMahon MB, Luster DG. Plant pathogenic fungi are harbored as endophytes in Rhododendron spp. native to the Eastern U.S.A. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Farinas C, Jourdan PS, Paul PA, Slot JC, Daughtrey ML, Ganeshan VD, Baysal-Gurel F, Hand FP. Phlox Species Show Quantitative and Qualitative Resistance to a Population of Powdery Mildew Isolates from the Eastern United States. PHYTOPATHOLOGY 2020; 110:1410-1418. [PMID: 32252592 DOI: 10.1094/phyto-12-19-0473-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: 06/11/2023]
Abstract
Ornamental plants in the genus Phlox are extensively planted in landscapes and home gardens around the world. A major limitation to a more widespread use of these plants is their susceptibility to powdery mildew (PM). In this study, we used multilocus sequence typing (MLST) analysis to gain insights into the population diversity of 32 Phlox PM pathogen (Golovinomyces magnicellulatus and Podosphaera sp.) isolates collected from the eastern United States and relate it to the ability to overcome host resistance. Low genetic diversity and a lack of structure were found within our population. Whole genome comparison of two isolates was used to support low genetic diversity evidence found with the MLST analysis. Recombination was suggested by the incongruences observed in the six phylogenetic trees generated from the housekeeping genes TEF-1α, CSI, ITS, IGS, H3, and TUB. Contrasting with low genetic diversity, we found high phenotypic diversity when using 10 of the 32 isolates to evaluate host resistance in four different Phlox species (P. paniculata 'Dunbar Creek', P. amoena OPGC 3598, P. glaberrima OPGC 3594, and P. subulata OPGC 4185) using in vitro bioassays. We observed quantitative and qualitative resistance in all Phlox species and a consistent low disease severity in our control, P. paniculata 'Dunbar Creek'. Taken together, the results generated in this study constitute a robust screening of popular Phlox germplasm that can be incorporated into breeding programs for PM resistance and provides significant information on the evolution of PM pathogens.
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Affiliation(s)
- Coralie Farinas
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
| | - Pablo S Jourdan
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210
| | - Pierce A Paul
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
| | - Margery L Daughtrey
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901
| | - Veena Devi Ganeshan
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, Tennessee State University, McMinnville, TN 37110
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Latorre SM, Reyes-Avila CS, Malmgren A, Win J, Kamoun S, Burbano HA. Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus. BMC Biol 2020; 18:88. [PMID: 32677941 PMCID: PMC7364606 DOI: 10.1186/s12915-020-00818-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae-the causal agent of blast disease of cereals- is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat, and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined the two largest genomic datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries. RESULTS The global population of the rice blast fungus consists mainly of three well-defined genetic groups and a diverse set of individuals. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in Southeast Asia followed by three independent clonal expansions that took place over the last ~ 200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence and absence of candidate effector genes. These genes encode secreted proteins that modulate plant defense and allow pathogen colonization. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of presence and absence of effector genes define each of the pandemic clonal lineages. CONCLUSIONS Our analyses reconstruct the genetic history of the rice-infecting lineage of M. oryzae revealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence and absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.
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Affiliation(s)
- Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - C Sarai Reyes-Avila
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Angus Malmgren
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tuebingen, Germany.
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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18
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Gent DH, Claassen BJ, Gadoury DM, Grünwald NJ, Knaus BJ, Radišek S, Weldon W, Wiseman MS, Wolfenbarger SN. Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. PHYTOPATHOLOGY 2020; 110:1105-1116. [PMID: 32091314 DOI: 10.1094/phyto-12-19-0448-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop. The disease was first reported in the Pacific Northwestern United States, the primary hop-growing region in this country, in the mid-1990s. More recently, the disease has reemerged in newly planted hopyards of the eastern United States, as hop production has expanded to meet demands of local craft brewers. The spread of strains virulent on previously resistant cultivars, the paucity of available fungicides, and the potential introduction of the MAT1-2 mating type to the western United States, all threaten sustainability of hop production. We sequenced the transcriptome of 104 isolates of P. macularis collected throughout the western United States, eastern United States, and Europe to quantify genetic diversity of pathogen populations and elucidate the possible origins of pathogen populations in the western United States. Discriminant analysis of principal components grouped isolates within three to five geographic populations, dependent on stringency of grouping criteria. Isolates from the western United States were phenotyped and categorized into one of three pathogenic races based on disease symptoms generated on differential cultivars. Western U.S. populations were clonal, irrespective of pathogenic race, and grouped with isolates originating from Europe. Isolates originating from wild hop plants in the eastern United States were genetically differentiated from all other populations, whereas isolates from cultivated hop plants in the eastern United States mostly grouped with isolates originating from the west, consistent with origins from nursery sources. Mating types of isolates originating from cultivated western and eastern U.S. hop plants were entirely MAT1-1. In contrast, a 1:1 ratio of MAT1-1 and MAT1-2 was observed with isolates sampled from wild plants or Europe. Within the western United States a set of highly differentiated loci were identified in P. macularis isolates associated with virulence to the powdery mildew R-gene R6. The weight of genetic and phenotypic evidence suggests a European origin of the P. macularis populations in the western United States, followed by spread of the pathogen from the western United States to re-emergent production regions in the eastern United States. Furthermore, R6 compatibility appears to have been selected from an extant isolate within the western United States. Greater emphasis on sanitation measures during propagation and quarantine policies should be considered to limit further spread of novel genotypes of the pathogen, both between and within production areas.
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Affiliation(s)
- David H Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Briana J Claassen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - David M Gadoury
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330, U.S.A
| | - Brian J Knaus
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | | | - William Weldon
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Michele S Wiseman
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - Sierra N Wolfenbarger
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
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19
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Fungal Evolution in Anthropogenic Environments: Botrytis cinerea Populations Infecting Small Fruit Hosts in the Pacific Northwest Rapidly Adapt to Human-Induced Selection Pressures. Appl Environ Microbiol 2020; 86:AEM.02908-19. [PMID: 32086310 DOI: 10.1128/aem.02908-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022] Open
Abstract
Many fungal pathogens have short generation times, large population sizes, and mixed reproductive systems, providing high potential to adapt to heterogeneous environments of agroecosystems. Such adaptation complicates disease management and threatens food production. A better understanding of pathogen population biology in such environments is important to reveal key aspects of adaptive divergence processes to allow improved disease management. Here, we studied how evolutionary forces shape population structure of Botrytis cinerea, the causal agent of gray mold, in the Pacific Northwest agroecosystems. Populations of B. cinerea from adjacent fields of small fruit hosts were characterized by combining neutral markers (microsatellites) with markers that directly respond to human-induced selection pressures (fungicide resistance). Populations were diverse, without evidence for recombination and association of pathogen genotype with host. Populations were highly localized with limited migration even among adjacent fields within a farm. A fungicide resistance marker revealed strong selection on population structure due to fungicide use. We found no association of resistance allele with genetic background, suggesting de novo development of fungicide resistance and frequent extinction/recolonization events by different genotypes rather than the spread of resistance alleles among fields via migration of a dominant genotype. Overall our results showed that in agroecosystems, B. cinerea populations respond strongly to selection by fungicide use with greater effect on population structure compared to adaptation to host plant species. This knowledge will be used to improve disease management by developing strategies that limit pathogen local adaptation to fungicides and other human-induced selection pressures present in Pacific Northwest agroecosystems and elsewhere.IMPORTANCE Agroecosystems represent an efficient model for studying fungal adaptation and evolution in anthropogenic environments. In this work, we studied what evolutionary forces shape populations of one of the most important fungal plant pathogens, B. cinerea, in small fruit agroecosystems of the Pacific Northwest. We hypothesized that host, geographic, and anthropogenic factors of agroecosystems structure B. cinerea populations. By combining neutral markers with markers that directly respond to human-induced selection pressures, we show that pathogen populations are highly localized and that selection pressure caused by fungicide use can have a greater effect on population structure than adaptation to host. Our results give a better understanding of population biology and evolution of this important plant pathogen in heterogeneous environments but also provide a practical framework for the development of efficient management strategies by limiting pathogen adaptation to fungicides and other human-induced selection pressures present in agroecosystems of the Pacific Northwest and elsewhere.
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20
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Diao Y, Larsen MM, Kamvar ZN, Zhang C, Li S, Wang W, Lin D, Peng Q, Knaus BJ, Foster ZSL, Grünwald NJ, Liu X. Genetic Differentiation and Clonal Expansion of Chinese Botrytis cinerea Populations from Tomato and Other Crops in China. PHYTOPATHOLOGY 2020; 110:428-439. [PMID: 31454305 DOI: 10.1094/phyto-09-18-0347-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Botrytis cinerea is an important pathogen of vegetable and fruit crops but little is known about its population structure and genetics in China. We hypothesized that the geographic populations of B. cinerea in China would be genetically differentiated by host, geographic location, and/or year. In this study, we collected 393 B. cinerea isolates representing 28 populations from tomato, cherry, and nectarine from 2006 to 2014 in China. The isolates were analyzed using 14 microsatellite markers, including six new markers that provided more genotyping power than the eight previously published loci. We also investigated the B. cinerea population structure and inferred its mode of reproduction and dispersal based on genotype data. High genotypic diversity was detected in all populations, and clonal reproduction was dominant. Southern China populations harbored more genotypes than northern populations. Differentiation by host plant was evident. Between 2011 and 2012, genotypes changed only slightly among years for Liaoning populations, but they changed substantially among years for the Shanghai and Fujian populations. Clonal dispersal was detected and the farthest dispersal distance was estimated to be about 1,717 km. Two high-frequency genotypes were widely distributed in more than 10 populations and across several years. Our results provide useful, novel information for plant breeding programs and control of B. cinerea in China.
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Affiliation(s)
- Yongzhao Diao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, U.S.A
| | - Meredith M Larsen
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Zhian N Kamvar
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, U.S.A
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
| | - Shuo Li
- China Animal Disease Control Center, Beijing, China 100125
| | - Weizhen Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
| | - Dong Lin
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
| | - Qin Peng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
| | - Brian J Knaus
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Zachary S L Foster
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China 100193
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21
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Wyman CR, Hadziabdic D, Boggess SL, Rinehart TA, Windham AS, Wadl PA, Trigiano RN. Low Genetic Diversity Suggests the Recent Introduction of Dogwood Powdery Mildew to North America. PLANT DISEASE 2019; 103:2903-2912. [PMID: 31449437 DOI: 10.1094/pdis-01-19-0051-re] [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: 06/10/2023]
Abstract
Cornus florida (flowering dogwood) is a popular understory tree endemic to the eastern hardwood forests of the United States. In 1996, dogwood powdery mildew caused by Erysiphe pulchra, an obligate biotrophic fungus of large bracted dogwoods, reached epidemic levels throughout the C. florida growing region. In the late 1990s, both sexual and asexual stages of E. pulchra were regularly observed; thereafter, the sexual stage was found less frequently. We examined the genetic diversity and population structure of 167 E. pulchra samples on C. florida leaves using 15 microsatellite loci. Samples were organized into two separate collection zone data sets, separated as eight zones and two zones, for the subsequent analysis of microsatellite allele length data. Clone correction analysis reduced the sample size to 90 multilocus haplotypes. Our study indicated low genetic diversity, a lack of definitive population structure, low genetic distance among multilocus haplotypes, and significant linkage disequilibrium among zones. Evidence of a population bottleneck was also detected. The results of our study indicated a high probability that E. pulchra reproduces predominately via asexual conidia and lend support to the hypothesis that E. pulchra is an exotic pathogen to North America.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christopher R Wyman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Timothy A Rinehart
- United States Department of Agriculture, Agriculture Research Service, Crop Production and Protection, Beltsville, MD 20705
| | - Alan S Windham
- Department of Entomology and Plant Pathology, University of Tennessee, Soil, Plant, and Pest Center, 5201 Marchant Drive, Nashville, TN 37211
| | - Phillip A Wadl
- United States Department of Agriculture, Agriculture Research Service, U.S. Vegetable Research, Charleston, SC 29414
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
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22
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Grünwald NJ, LeBoldus JM, Hamelin RC. Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:301-321. [PMID: 31226018 DOI: 10.1146/annurev-phyto-082718-100117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sudden oak and sudden larch death pathogen Phytophthora ramorum emerged simultaneously in the United States on oak and in Europe on Rhododendron in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for P. ramorum have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of P. ramorum in Asia provide renewed impetus for research on the sudden oak death pathogen.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA;
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Faculté de Foresterie et de Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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23
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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: 6] [Impact Index Per Article: 1.0] [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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Peterson EK, Larson ER, Parke JL. Film-Forming Polymers and Surfactants Reduce Infection and Sporulation of Phytophthora ramorum on Rhododendron. PLANT DISEASE 2019; 103:1148-1155. [PMID: 30964419 DOI: 10.1094/pdis-05-18-0802-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum, cause of sudden oak death and ramorum leaf blight, can persist undetected in infested nurseries. Many conventional fungicides are effective in reducing or delaying symptom expression but some may confound visual detection of infected plants. We tested film-forming polymers (FFPs) and surfactants for their ability to reduce infection and sporulation of P. ramorum on rhododendron. FFPs (Anti-Stress, Moisturin, Nature Shield, Nu-Film, and Vapor Gard) and surfactants (Tergitol, Zonix, and an unregistered AGAE product) were screened in detached-leaf assays. Anti-Stress, Nu-Film, Zonix, and a Nu-Film-Zonix mixture were additionally tested for durability, protection against exposure to infested water, and a reduction in sporulation. FFP effectiveness was retained for at least 3 weeks of exposure to overhead irrigation and rain. Relative to controls, foliar treatments protected rhododendron branches exposed to infested water. No treatments prevented symptom development when applied postinfection but leaves treated with Anti-Stress, Zonix, and the Nu-Film-Zonix mixture produced significantly fewer sporangia relative to controls. Application of FFPs and surfactants to quarantined, potentially infected plants offers a management tool for reducing infection and sporulation but not symptom expression, thereby limiting disease spread without interfering with disease detection.
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Affiliation(s)
- Ebba K Peterson
- 1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; and
| | - Eric R Larson
- 2 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Jennifer L Parke
- 1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; and
- 2 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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Dale AL, Feau N, Everhart SE, Dhillon B, Wong B, Sheppard J, Bilodeau GJ, Brar A, Tabima JF, Shen D, Brasier CM, Tyler BM, Grünwald NJ, Hamelin RC. Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio 2019; 10:e02452-18. [PMID: 30862749 PMCID: PMC6414701 DOI: 10.1128/mbio.02452-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.IMPORTANCE Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.
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Affiliation(s)
- Angela L Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- GC-New Construction Materials, FPInnovations, Vancouver, British Columbia, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barbara Wong
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
| | - Julie Sheppard
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Avneet Brar
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Clive M Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
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Huzar-Novakowiski J, Dorrance AE. Genetic Diversity and Population Structure of Pythium irregulare from Soybean and Corn Production Fields in Ohio. PLANT DISEASE 2018; 102:1989-2000. [PMID: 30124360 DOI: 10.1094/pdis-11-17-1725-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
High levels of genetic diversity have been described within the Pythium irregulare complex from several host plants; however, little is known about the population structure in fields used for grain production. Therefore, the objective of this study was to evaluate the genetic diversity and population structure of 53 isolates baited from 28 soybean and corn production fields from 25 counties in Ohio. Genetic diversity was characterized based on sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and with 21 simple sequence repeat (SSR) markers. In addition, aggressiveness on soybean, optimum growth temperature, and sensitivity to metalaxyl fungicide were determined. ITS sequence analysis indicated that four isolates clustered with P. cryptoirregulare, whereas the remaining isolates clustered with P. irregulare that was subdivided into two groups (1 and 2). Cluster analysis of SSR data revealed a similar subdivision, which was also supported by structure analysis. The isolates from group 2 grew at a slower rate, but both groups of P. irregulare and P. cryptoirregulare recovered in this study had the same optimum growth at 27°C. Variability of aggressiveness and sensitivity toward metalaxyl fungicide was also observed among isolates within each group. The results from this study will help in the selection of isolates to be used in screening for resistance, assessment of fungicide efficacy, and disease management recommendations.
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Affiliation(s)
- J Huzar-Novakowiski
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - A E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
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Changes in the population structure and sporulation behaviour of Phytophthora ramorum associated with the epidemic on Larix (larch) in Britain. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1702-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Funahashi F, Parke JL. Thermal Inactivation of Inoculum of Two Phytophthora Species by Intermittent Versus Constant Heat. PHYTOPATHOLOGY 2018; 108:829-836. [PMID: 29384447 DOI: 10.1094/phyto-06-17-0205-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Research on solarization efficacy has examined the critical temperature and minimum exposure time to inactivate soilborne pathogens. Most mathematical models focus on survival of inoculum subjected to a constant heat regime rather than an intermittent heat regime that better simulates field conditions. To develop a more accurate predictive model, we conducted controlled lab experiments with rhododendron leaf disks infested with Phytophthora ramorum and P. pini. Focused in vitro experiments with P. ramorum showed significantly longer survival of inoculum exposed to intermittent versus constant heat, indicating that intermittent heat is less damaging. A similar trend was observed in soil. Damage was evaluated by comparing the reduction in subsequent survival time of inoculum subjected to different intensities of sublethal heat treatments. Inoculum exposure to continuous heat reflected an increasing rate of damage accumulation. Multiple sublethal heat events resulted in a constant rate of damage accumulation which allowed us to calculate total damage as the sum of damage from each heat event. A model including a correction for an intermittent heat regime significantly improved the prediction of thermal inactivation under a temperature regime that simulated field conditions.
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Affiliation(s)
- Fumiaki Funahashi
- Department of Crop and Soil Science, Oregon State University, Corvallis 97331
| | - Jennifer L Parke
- Department of Crop and Soil Science, Oregon State University, Corvallis 97331
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la Bastide PYD, Naumann C, Hintz WE. Assessment of intra-specific variability in Saprolegnia parasitica populations of aquaculture facilities in British Columbia, Canada. DISEASES OF AQUATIC ORGANISMS 2018; 128:235-248. [PMID: 29862981 DOI: 10.3354/dao03224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Among the Saprolegnia species found in aquaculture facilities, S. parasitica is recognized as the primary fish pathogen and remains an ongoing concern in fish health management. Until recently, these pathogens were kept in check by use of malachite green; due to its toxicity, this chemical has now been banned from use in many countries. It is difficult to predict and control S. parasitica outbreaks in freshwater systems and there is a need to understand the population genetic structure of this pathogen. Genetic characterization of this species in aquaculture systems would provide information to track introductions and determine possible sources of inoculum. Degenerate PCR primers containing short sequence repeats were used to create microsatellite-associated genetic markers (random amplified microsatellites) for the comparison of S. parasitica isolates collected primarily from commercial Atlantic salmon aquaculture systems in British Columbia, Canada, over a 15 mo period to describe their spatial and temporal variability. The frequencies of amplified products were compared and the population genetic diversity was measured using Nei's genetic distance and Shannon's information index, while the species population structure was evaluated by phylogenetic analysis. S. parasitica was detected in all facilities sampled. Genetic diversity was low but not clonal, most likely due to repeated introduction events and a low level of sexual recombination over time. A better understanding of pathogen population structure will assist the development of effective preventative measures and targeted treatments for disease outbreaks.
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Affiliation(s)
- Paul Y de la Bastide
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
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McCartney MM, Roubtsova TV, Yamaguchi MS, Kasuga T, Ebeler SE, Davis CE, Bostock RM. Effects of Phytophthora ramorum on volatile organic compound emissions of Rhododendron using gas chromatography-mass spectrometry. Anal Bioanal Chem 2017; 410:1475-1487. [PMID: 29247382 DOI: 10.1007/s00216-017-0789-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Phytophthora ramorum is an invasive and devastating plant pathogen that causes sudden oak death in coastal forests in the western United States and ramorum blight in nursery ornamentals and native plants in various landscapes. As a broad host-range quarantine pest that can be asymptomatic in some hosts, P. ramorum presents significant challenges for regulatory efforts to detect and contain it, particularly in commercial nurseries. As part of a program to develop new detection methods for cryptic infections in nursery stock, we compared volatile emissions of P. ramorum-inoculated and noninoculated Rhododendron plants using three gas chromatography-mass spectrometry methods. The first used a branch enclosure combined with headspace sorptive extraction to measure plant volatiles in situ. Seventy-eight compounds were found in the general Rhododendron profile. The volatile profile of inoculated but asymptomatic plants (121 days post-inoculation) was distinguishable from the profile of the noninoculated controls. Three compounds were less abundant in inoculated Rhododendron plants relative to noninoculated and mock-inoculated control plants. A second method employed stir bar sorptive extraction to measure volatiles in vitro from leaf extractions in methanol; 114 volatiles were found in the overall profile with 30 compounds less abundant and one compound more abundant in inoculated Rhododendron plants relative to mock-inoculated plants. At 128 days post-inoculation, plants were asymptomatic and similar in appearance to the noninoculated controls, but their chemical profiles were different. In a third technique, volatiles from water runoff from the soil of potted healthy and inoculated Rhododendron plants were compared. Runoff from the inoculated plants contained four unique volatile compounds that never appeared in the runoff from mock-inoculated plants. These three volatile detection techniques could lead to innovative approaches that augment detection and diagnosis of P. ramorum and oomycete pathogens in nurseries and other settings. Graphical abstract Detection of volatile signatures may aid in discriminating healthy vs. infected but asymptomatic plants in nursery and greenhouse facilities.
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Affiliation(s)
- Mitchel M McCartney
- Mechanical and Aerospace Engineering, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Tatiana V Roubtsova
- Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Mei S Yamaguchi
- Mechanical and Aerospace Engineering, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA, 95616, USA
| | - Susan E Ebeler
- Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Cristina E Davis
- Mechanical and Aerospace Engineering, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Richard M Bostock
- Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Grünwald NJ, Everhart SE, Knaus BJ, Kamvar ZN. Best Practices for Population Genetic Analyses. PHYTOPATHOLOGY 2017; 107:1000-1010. [PMID: 28513284 DOI: 10.1094/phyto-12-16-0425-rvw] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.
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Affiliation(s)
- N J Grünwald
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - S E Everhart
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - B J Knaus
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - Z N Kamvar
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
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Mantooth K, Hadziabdic D, Boggess S, Windham M, Miller S, Cai G, Spatafora J, Zhang N, Staton M, Ownley B, Trigiano R. Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America. PLoS One 2017; 12:e0180345. [PMID: 28746379 PMCID: PMC5528261 DOI: 10.1371/journal.pone.0180345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/14/2017] [Indexed: 11/19/2022] Open
Abstract
Cornus florida (flowering dogwood) and C. nuttallii (Pacific dogwood) are North American native tree species that belong to the big-bracted group of dogwoods. Cornus species are highly valued for their ornamental characteristics, and have fruits that contain high fat content for animals. Also, they are an important understory tree in natural forests. Dogwood anthracnose, caused by Discula destructiva, was observed in the late 1970s on the east and west coasts of the United States and by 1991 had quickly spread throughout most of the native ranges of C. florida and C. nuttalli. We investigated the genetic diversity and population structure of 93 D. destructiva isolates using 47 microsatellite loci developed from the sequenced genome of the type strain of D. destructiva. Clone-corrected data indicated low genetic diversity and the presence of four genetic clusters that corresponded to two major geographic areas, the eastern United States and the Pacific Northwest, and to the two collection time periods when the isolates were collected (pre- and post-1993). Linkage disequilibrium was present in five out of six subpopulations, suggesting that the fungus only reproduced asexually. Evidence of population bottlenecks was indicated across four identified genetic clusters, and was probably the result of the limited number of founding individuals on both coasts. These results support the hypothesis that D. destructiva is an exotic pathogen with independent introductions on the east and west coasts of North America. We also tested the cross-amplification of these microsatellite primers to other Discula species. Genomic DNA from 17 isolates of four other Discula species and two isolates of Juglanconis species (formerly Melanconis species) were amplified by 17 of 47 primer pairs. These primers may be useful for investigating the genetic diversity and population structure of these Discula species.
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Affiliation(s)
- Kristie Mantooth
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sarah Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mark Windham
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Stephen Miller
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
- APHIS PPQ, Linden, New Jersey, United States of America
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture, West Lafayette, Indiana, United States of America
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Joseph Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Ning Zhang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Meg Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bonnie Ownley
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Robert Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Gagnon MC, Feau N, Dale AL, Dhillon B, Hamelin RC, Brasier CM, Grünwald NJ, Brière SC, Bilodeau GJ. Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data. PLANT DISEASE 2017; 101:666-673. [PMID: 30678572 DOI: 10.1094/pdis-11-16-1586-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.
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Affiliation(s)
| | - Nicolas Feau
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Angela L Dale
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Braham Dhillon
- UBC and Department of Plant Pathology, University of Arkansas, Fayetteville
| | - Richard C Hamelin
- UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Derevnina L, Petre B, Kellner R, Dagdas YF, Sarowar MN, Giannakopoulou A, De la Concepcion JC, Chaparro-Garcia A, Pennington HG, van West P, Kamoun S. Emerging oomycete threats to plants and animals. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150459. [PMID: 28080985 PMCID: PMC5095538 DOI: 10.1098/rstb.2015.0459] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica and Halioticida noduliformans For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Lida Derevnina
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Yasin F Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mohammad Nasif Sarowar
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | | | | | | | | | - Pieter van West
- International Centre for Aquaculture Research and Development, Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
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Biasi A, Martin FN, Cacciola SO, di San Lio GM, Grünwald NJ, Schena L. Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers. PHYTOPATHOLOGY 2016; 106:1006-14. [PMID: 27111805 DOI: 10.1094/phyto-11-15-0299-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In all, 231 isolates of Phytophthora nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa, and Ruta), and other plant genera were characterized using simple-sequence repeat markers. In total, 99 multilocus genotypes (MLG) were identified, revealing a strong association between genetic grouping and host of recovery, with most MLG being associated with a single host genus. Significant differences in the structure of populations were revealed but clonality prevailed in all populations. Isolates from Citrus were found to be genetically related regardless of their geographic origin and were characterized by high genetic uniformity and high inbreeding coefficients. Higher variability was observed for other populations and a significant geographical structuring was determined for isolates from Nicotiana. Detected differences were related to the propagation and cultivation systems of different crops. Isolates obtained from Citrus spp. are more likely to be distributed worldwide with infected plant material whereas Nicotiana and Lycopersicon spp. are propagated by seed, which would not contribute to the spread of the pathogen and result in a greater chance for geographic isolation of lineages. With regard to ornamental species in nurseries, the high genetic variation is likely the result of the admixture of diverse pathogen genotypes through the trade of infected plant material from various geographic origins, the presence of several hosts in the same nursery, and genetic recombination through sexual reproduction of this heterothallic species.
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Affiliation(s)
- Antonio Biasi
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
| | - Frank N Martin
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
| | - Santa O Cacciola
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
| | - Gaetano Magnano di San Lio
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
| | - Niklaus J Grünwald
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
| | - Leonardo Schena
- First, fourth, and sixth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 East Alisal Street, Salinas, CA 93905; third author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy; and fifth author: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR
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Grünwald NJ, McDonald BA, Milgroom MG. Population Genomics of Fungal and Oomycete Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:323-46. [PMID: 27296138 DOI: 10.1146/annurev-phyto-080614-115913] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We are entering a new era in plant pathology in which whole-genome sequences of many individuals of a pathogen species are becoming readily available. Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization, as genome sequences or large numbers of single nucleotide polymorphisms become readily available from multiple individuals of the same species. This emerging field encompasses detailed genetic analyses of natural populations, comparative genomic analyses of closely related species, identification of genes under selection, and linkage analyses involving association studies in natural populations or segregating populations resulting from crosses. The era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. This review focuses on conceptual and methodological issues as well as the approaches to answering questions in population genomics. The major steps start with defining relevant biological and evolutionary questions, followed by sampling, genotyping, and phenotyping, and ending in analytical methods and interpretations. We provide examples of recent applications of population genomics to fungal and oomycete plant pathogens.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330;
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853;
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland;
| | - Michael G Milgroom
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853;
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Tooley PW, Browning M, Shishkoff N. Pyracantha 'Mohave' Fruit Infection by Phytophthora ramorum and Transmission of the Pathogen from Infected Fruit to Roots of Viburnum tinus. PLANT DISEASE 2016; 100:555-560. [PMID: 30688592 DOI: 10.1094/pdis-03-15-0369-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colonization of the fleshy fruit of Cornus florida, C. kousa, Laurus nobilis, Malus hupehensis, and Pyracantha 'Mohave' was observed following inoculation with sporangia of Phytophthora ramorum. However, abundant production of chlamydospores was only observed in the fruit of Pyracantha 'Mohave'. Pyracantha 'Mohave' fruit that had been inoculated with a P. ramorum sporangia suspension were placed in pots containing rooted cuttings of Viburnum tinus in a misting tent or in water-filled trays in a climate-controlled greenhouse. Runoff was collected for 24 to 30 days, and roots were plated after the final collection. Mean percent recovery from infected roots was not significantly different (P = 0.05, Tukey's test) between bottom-watered treatments in trays and misted treatments, averaging 58% for bottom-watered and 54% for mist treatments. The number of CFU collected in runoff from bottom-watered plants was consistently lower than that obtained from plants held under mist, likely due to desiccation of the fruit. The results show that root infection of V. tinus can occur by P. ramorum via infected fruit of Pyracantha 'Mohave'. This phenomenon represents a pathway of infection for P. ramorum not previously reported, which may play a role in disease epidemiology.
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Affiliation(s)
- Paul W Tooley
- United States Department of Agriculture-Agricultural Research Service Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702
| | - Marsha Browning
- United States Department of Agriculture-Agricultural Research Service Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702
| | - Nina Shishkoff
- United States Department of Agriculture-Agricultural Research Service Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702
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Funahashi F, Parke JL. Effects of Soil Solarization and Trichoderma asperellum on Soilborne Inoculum of Phytophthora ramorum and Phytophthora pini in Container Nurseries. PLANT DISEASE 2016; 100:438-443. [PMID: 30694147 DOI: 10.1094/pdis-04-15-0453-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Infested container nursery beds are an important source of soilborne Phytophthora spp. for initiating disease through movement with surface water or splashing onto foliage. We investigated the effects of soil solarization, alone or with subsequent amendment with a Trichoderma asperellum biocontrol agent, on the survival of Phytophthora spp. inoculum. In field trials conducted with Phytophthora ramorum in San Rafael, CA and with P. pini in Corvallis, OR, infested rhododendron leaf inoculum was buried at 5, 15, and 30 cm below the soil surface. Solarization for 2 or 4 weeks during summer 2012 eliminated recovery of Phytophthora spp. buried at all depths in California trial 1, at 5 and 15 cm in California trial 2, but only at 5 cm in Oregon. There was no significant reduction of Phytophthora spp. recovery after T. asperellum application. Although the population densities of the introduced T. asperellum at the 5-cm depth were often two- to fourfold higher in solarized compared with nonsolarized plots, they were not significantly different (P = 0.052). Soil solarization appears to be a promising technique for disinfesting the upper layer of soil in container nurseries under certain conditions.
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Affiliation(s)
| | - J L Parke
- Department of Crop and Soil Science and Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331
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41
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Effectiveness of dynamic quarantines against pathogen spread in models of the horticultural trade network. ECOLOGICAL COMPLEXITY 2015. [DOI: 10.1016/j.ecocom.2015.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Knaus BJ, Fieland VJ, Graham KA, Grünwald NJ. Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries. PLANT DISEASE 2015; 99:1326-1332. [PMID: 30690987 DOI: 10.1094/pdis-09-14-0964-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.
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Affiliation(s)
- B J Knaus
- Horticultural Crops Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR
| | - V J Fieland
- Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - K A Graham
- Horticultural Crops Research Unit, USDA-ARS, Corvallis, OR
| | - N J Grünwald
- Horticultural Crops Research Unit, USDA-ARS, and Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis
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Migliorini D, Ghelardini L, Tondini E, Luchi N, Santini A. The potential of symptomless potted plants for carrying invasive soilborne plant pathogens. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12347] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Duccio Migliorini
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente DiSPAA; Università di Firenze; Piazzale delle Cascine 28 50144 Firenze Italy
| | - Luisa Ghelardini
- Institute for Sustainable Plant Protection IPSP; National Research Council C.N.R.; Via Madonna del Piano 10 50019 Sesto Fiorentino Italy
| | - Elena Tondini
- Institute for Sustainable Plant Protection IPSP; National Research Council C.N.R.; Via Madonna del Piano 10 50019 Sesto Fiorentino Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection IPSP; National Research Council C.N.R.; Via Madonna del Piano 10 50019 Sesto Fiorentino Italy
| | - Alberto Santini
- Institute for Sustainable Plant Protection IPSP; National Research Council C.N.R.; Via Madonna del Piano 10 50019 Sesto Fiorentino Italy
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Kamvar ZN, Larsen MM, Kanaskie AM, Hansen EM, Grünwald NJ. Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests. PHYTOPATHOLOGY 2015; 105:982-989. [PMID: 26068281 DOI: 10.1094/phyto-12-14-0350-fi] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled symptomatic tanoak trees from 2001 to the present. Populations sampled over this period were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. The original introduction into the Joe Hall area eventually spread to several regions: mostly north but also east and southwest. A new introduction into Hunter Creek appears to correspond to a second introduction not clustering with the early introduction. Our data are best explained by both introductions originating from nursery populations in California or Oregon and resulting from two distinct introduction events. Continued vigilance and eradication of nursery populations of P. ramorum are important to avoid further emergence and potential introduction of other clonal lineages.
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Affiliation(s)
- Z N Kamvar
- First and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis; second and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR; third author: Oregon Department of Forestry, Salem; and fifth author: Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis
| | - M M Larsen
- First and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis; second and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR; third author: Oregon Department of Forestry, Salem; and fifth author: Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis
| | - A M Kanaskie
- First and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis; second and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR; third author: Oregon Department of Forestry, Salem; and fifth author: Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis
| | - E M Hansen
- First and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis; second and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR; third author: Oregon Department of Forestry, Salem; and fifth author: Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis
| | - N J Grünwald
- First and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis; second and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR; third author: Oregon Department of Forestry, Salem; and fifth author: Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis
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Kamvar ZN, Brooks JC, Grünwald NJ. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front Genet 2015; 6:208. [PMID: 26113860 PMCID: PMC4462096 DOI: 10.3389/fgene.2015.00208] [Citation(s) in RCA: 457] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.
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Affiliation(s)
- Zhian N. Kamvar
- Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Jonah C. Brooks
- College of Electrical Engineering and Computer Science, Oregon State UniversityCorvallis, OR, USA
| | - Niklaus J. Grünwald
- Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Horticultural Crops Research Laboratory, USDA Agricultural Research ServiceCorvallis, OR, USA
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Abstract
Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.
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Affiliation(s)
- Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611;
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Kamoun S, Furzer O, Jones JDG, Judelson HS, Ali GS, Dalio RJD, Roy SG, Schena L, Zambounis A, Panabières F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grünwald NJ, Mukhtar MS, Tomé DFA, Tör M, Van Den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJG, Petre B, Ristaino J, Yoshida K, Birch PRJ, Govers F. The Top 10 oomycete pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2015; 16:413-34. [PMID: 25178392 PMCID: PMC6638381 DOI: 10.1111/mpp.12190] [Citation(s) in RCA: 516] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
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Affiliation(s)
- Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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Short DPG, Gurung S, Koike ST, Klosterman SJ, Subbarao KV. Frequency of Verticillium Species in Commercial Spinach Fields and Transmission of V. dahliae from Spinach to Subsequent Lettuce Crops. PHYTOPATHOLOGY 2015; 105:80-90. [PMID: 25098494 DOI: 10.1094/phyto-02-14-0046-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Verticillium wilt caused by V. dahliae is a devastating disease of lettuce in California (CA). The disease is currently restricted to a small geographic area in central coastal CA, even though cropping patterns in other coastal lettuce production regions in the state are similar. Infested spinach seed has been implicated in the introduction of V. dahliae into lettuce fields but direct evidence linking this inoculum to wilt epidemics in lettuce is lacking. In this study, 100 commercial spinach fields in four coastal CA counties were surveyed to evaluate the frequency of Verticillium species recovered from spinach seedlings and the area under spinach production in each county was assessed. Regardless of the county, V. isaacii was the most frequently isolated species from spinach followed by V. dahliae and, less frequently, V. klebahnii. The frequency of recovery of Verticillium species was unrelated to the occurrence of Verticillium wilt on lettuce in the four counties but was related to the area under spinach production in individual counties. The transmission of V. dahliae from infested spinach seeds to lettuce was investigated in microplots. Verticillium wilt developed on lettuce following two or three plantings of Verticillium-infested spinach, in independent experiments. The pathogen recovered from the infected lettuce from microplots was confirmed as V. dahliae by polymerase chain reaction assays. In a greenhouse study, transmission of a green fluorescence protein-tagged mutant strain of V. dahliae from spinach to lettuce roots was demonstrated, after two cycles of incorporation of infected spinach residue into the soil. This study presents conclusive evidence that V. dahliae introduced via spinach seed can cause Verticillium wilt in lettuce.
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Eyre CA, Hayden KJ, Kozanitas M, Grünwald NJ, Garbelotto M. Lineage, Temperature, and Host Species have Interacting Effects on Lesion Development in Phytophthora ramorum. PLANT DISEASE 2014; 98:1717-1727. [PMID: 30703894 DOI: 10.1094/pdis-02-14-0151-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
There are four recognized clonal lineages of the pathogen Phytophthora ramorum. The two major lineages present in North America are NA1 and NA2. With a few exceptions, NA1 is found in natural forest ecosystems and nurseries, and NA2 is generally restricted to nurseries. Isolates from the NA1 and NA2 lineages were used to infect rhododendron, camellia, and California bay laurel in detached leaf assays to study the effects of lineage, temperature, and host on pathogenicity and host susceptibility. Isolates within both lineages were highly variable in their ability to form lesions on each host. There was also a tendency toward reduced lesion size in successive trials, suggesting degeneration of isolates over time. Temperature had a significant effect on lesion size, with a response that varied depending on the host and isolate. Phenotypic differences between lineages appear to be heavily influenced by the representation of isolates used, host, and temperature. The importance of temperature, host, and lineage are discussed with respect to disease management, as well as future range expansions and migrations of the pathogen.
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Affiliation(s)
- C A Eyre
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley
| | - K J Hayden
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California-Berkeley; INRA, Interactions Arbres-Microorganismes, UMR1136, F-54280 Champenoux, France; and Université de Lorraine, Interactions Arbres-Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
| | - M Kozanitas
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California-Berkeley
| | - N J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR
| | - M Garbelotto
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California-Berkeley
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Parke JL, Knaus BJ, Fieland VJ, Lewis C, Grünwald NJ. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management. PHYTOPATHOLOGY 2014; 104:1052-1062. [PMID: 24702667 DOI: 10.1094/phyto-01-14-0014-r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33%), P. cinnamomi (26%), P. syringae (19%), and P. citrophthora (11%). From soil and gravel substrates, P. plurivora accounted for 25% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.
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