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Elameen A, de Labrouhe DT, Bret-Mestries E, Delmotte F. Spatial Genetic Structure and Pathogenic Race Composition at the Field Scale in the Sunflower Downy Mildew Pathogen, Plasmopara halstedii. J Fungi (Basel) 2022; 8:1084. [PMID: 36294648 PMCID: PMC9605284 DOI: 10.3390/jof8101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Yield losses in sunflower crops caused by Plasmopara halstedii can be up to 100%, depending on the cultivar susceptibility, environmental conditions, and virulence of the pathogen population. The aim of this study was to investigate the genetic and phenotypic structure of a sunflower downy mildew agent at the field scale. The genetic diversity of 250 P. halstedii isolates collected from one field in southern France was assessed using single-nucleotide polymorphisms (SNPs) and single sequence repeats (SSR). A total of 109 multilocus genotypes (MLG) were identified among the 250 isolates collected in the field. Four genotypes were repeated more than 20 times and spatially spread over the field. Estimates of genetic relationships among P. halstedii isolates using principal component analysis and a Bayesian clustering approach demonstrated that the isolates are grouped into two main genetic clusters. A high level of genetic differentiation among clusters was detected (FST = 0.35), indicating overall limited exchange between them, but our results also suggest that recombination between individuals of these groups is not rare. Genetic clusters were highly related to pathotypes, as previously described for this pathogen species. Eight different races were identified (100, 300, 304, 307, 703, 704, 707, and 714), with race 304 being predominant and present at most of the sites. The co-existence of multiple races at the field level is a new finding that could have important implications for the management of sunflower downy mildew. These data provide the first population-wide picture of the genetic structure of P. halstedii at a fine spatial scale.
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Affiliation(s)
- Abdelhameed Elameen
- NIBIO, Norwegian Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, N-1431 Ås, Norway
| | | | | | - Francois Delmotte
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, 33140 Villenave d’Ornon, France
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Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics. PLANTS 2021; 10:plants10030435. [PMID: 33668762 PMCID: PMC7996204 DOI: 10.3390/plants10030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/26/2022]
Abstract
Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.
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Gilley MA, Gulya TJ, Seiler GJ, Underwood W, Hulke BS, Misar CG, Markell SG. Determination of Virulence Phenotypes of Plasmopara halstedii in the United States. PLANT DISEASE 2020; 104:2823-2831. [PMID: 32955406 DOI: 10.1094/pdis-10-19-2063-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Downy mildew, caused by Plasmopara halstedii (Farl.) Berl. and de Toni, is an economically important disease in cultivated sunflowers, Helianthus annuus L. Resistance genes incorporated into commercial hybrids are used as an effective disease management tool, but the duration of effectiveness is limited as virulence evolves in the pathogen population. A comprehensive assessment of pathogen virulence was conducted in 2014 and 2015 in the U.S. Great Plains states of North Dakota and South Dakota, where approximately 75% of the U.S. sunflower is produced annually. The virulence phenotypes (and races) of 185 isolates were determined using the U.S. standard set of nine differentials. Additionally, the virulence phenotypes of 61 to 185 isolates were determined on 13 additional lines that have been used to evaluate pathogen virulence in North America and/or internationally. Although widespread virulence was identified on several genes, new virulence was identified on the Pl8 resistance gene, and no virulence was observed on the PlArg, Pl15, Pl17 and Pl18 genes. Results of this study suggest that three additional lines should be used as differentials and agree with previous studies that six lines proposed as differentials should be used in two internationally accepted differential sets. For effective disease management using genetic resistance, it is critical that virulence data be relevant and timely. This is best accomplished when pathogen virulence is determined frequently and by using genetic lines containing resistance genes actively incorporated into commercial cultivars.
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Affiliation(s)
- Michelle A Gilley
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | | | | | | | | | | | - Samuel G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
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Suo W, Shi X, Xu S, Li X, Lin Y. Towards low cost, multiplex clinical genotyping: 4-fluorescent Kompetitive Allele-Specific PCR and its application on pharmacogenetics. PLoS One 2020; 15:e0230445. [PMID: 32176732 PMCID: PMC7075562 DOI: 10.1371/journal.pone.0230445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/29/2020] [Indexed: 01/08/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) is associated with efficacy of specific drugs. Although there are several methods for SNP genotyping in clinical settings, alternative methods with lower cost, higher throughout and less complexity are still needed. In this study, we modified Kompetitive Allele Specific PCR to enable multiplex SNP genotyping by introducing additional fluorescent cassettes that specifically help to differentiate more amplification signals in a single reaction. This new format of assay achieved a limit of detection down to 310 copies/ reactions for simultaneous detection of 2 SNPs with only standard end-point PCR workflow for synthetic controls, and genotyped 117 clinical samples with results that were in 100% agreement with hospital reports. This study presented a simplified, cost-effective high-throughput SNP genotyping alternative for pharmacogenetic variants, and enabled easier access to pharmaceutical guidance when needed.
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Affiliation(s)
- Wei Suo
- Pharmacy Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xiujin Shi
- Pharmacy Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Sha Xu
- Pharmacy Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xiao Li
- Pharmacy Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yang Lin
- Pharmacy Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- * E-mail:
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Cohen Y, Rubin AE, Galperin M. Novel synergistic fungicidal mixtures of oxathiapiprolin protect sunflower seeds from downy mildew caused by Plasmopara halstedii. PLoS One 2019; 14:e0222827. [PMID: 31545821 PMCID: PMC6756549 DOI: 10.1371/journal.pone.0222827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/09/2019] [Indexed: 01/11/2023] Open
Abstract
Plenaris (oxathiapiprolin) applied to sunflower seedlings was highly effective in controlling downy mildew incited by the oomycete Plasmopara halstedii. In vitro assays revealed strong suppression of zoospore release and cystospore germination of P.halstedii by Plenaris. Bion (acibenzolar-S-methyl) and Apron (mefenoxam) were partially effective when used singly, but performed synergistically when mixed with Plenaris. Seed treatment (coating) with Plenaris provided dose-dependent control of the disease whereas Bion and Apron provided partial or poor control. However, seeds treated with mixtures containing reduced rates of Plenaris and full rates of Bion and/or Apron provided complete control of the disease due to the synergistic interaction between these components. Such mixtures should be used for seed treatment in the field to minimize selection pressure imposed on the pathogen.
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Affiliation(s)
- Yigal Cohen
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- * E-mail: ,
| | - Avia E. Rubin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Mariana Galperin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
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Pecrix Y, Buendia L, Penouilh‐Suzette C, Maréchaux M, Legrand L, Bouchez O, Rengel D, Gouzy J, Cottret L, Vear F, Godiard L. Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:730-748. [PMID: 30422341 PMCID: PMC6849628 DOI: 10.1111/tpj.14157] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 05/20/2023]
Abstract
Over the last 40 years, new sunflower downy mildew isolates (Plasmopara halstedii) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad-spectrum resistances. Here, 354 RXLR effectors defined in silico from our new genomic data were classified in a network of 40 connected components sharing conserved protein domains. Among 205 RXLR effector genes encoding conserved proteins in 17 P. halstedii pathotypes of varying virulence, we selected 30 effectors that were expressed during plant infection as potentially essential genes to target broad-spectrum resistance in sunflower. The transient expression of the 30 core effectors in sunflower and in Nicotiana benthamiana leaves revealed a wide diversity of targeted subcellular compartments, including organelles not so far shown to be targeted by oomycete effectors such as chloroplasts and processing bodies. More than half of the 30 core effectors were able to suppress pattern-triggered immunity in N. benthamiana, and five of these induced hypersensitive responses (HR) in sunflower broad-spectrum resistant lines. HR triggered by PhRXLRC01 co-segregated with Pl22 resistance in F3 populations and both traits localized in 1.7 Mb on chromosome 13 of the sunflower genome. Pl22 resistance was physically mapped on the sunflower genome recently sequenced, unlike all the other downy mildew resistances published so far. PhRXLRC01 and Pl22 are proposed as an avirulence/resistance gene couple not previously described in sunflower. Core effector recognition is a successful strategy to accelerate broad-spectrum resistance gene identification in complex crop genomes such as sunflower.
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Affiliation(s)
- Yann Pecrix
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Luis Buendia
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Charlotte Penouilh‐Suzette
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Maude Maréchaux
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Ludovic Legrand
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Olivier Bouchez
- GeT‐PlaGeUS INRA 1426INRA AuzevilleF‐31326Castanet‐Tolosan CedexFrance
| | - David Rengel
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Jérôme Gouzy
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Ludovic Cottret
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | | | - Laurence Godiard
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
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Crandall SG, Rahman A, Quesada-Ocampo LM, Martin FN, Bilodeau GJ, Miles TD. Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges. PLANT DISEASE 2018; 102:265-275. [PMID: 30673522 DOI: 10.1094/pdis-09-17-1455-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
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Affiliation(s)
- Sharifa G Crandall
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
| | - Alamgir Rahman
- North Carolina State University, Department of Plant Pathology, Raleigh, NC, 27695
| | | | - Frank N Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, 93905
| | | | - Timothy D Miles
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
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Gascuel Q, Buendia L, Pecrix Y, Blanchet N, Muños S, Vear F, Godiard L. RXLR and CRN Effectors from the Sunflower Downy Mildew Pathogen Plasmopara halstedii Induce Hypersensitive-Like Responses in Resistant Sunflower Lines. FRONTIERS IN PLANT SCIENCE 2016; 7:1887. [PMID: 28066456 PMCID: PMC5165252 DOI: 10.3389/fpls.2016.01887] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/29/2016] [Indexed: 05/20/2023]
Abstract
Plasmopara halstedii is an obligate biotrophic oomycete causing downy mildew disease on sunflower, Helianthus annuus, an economically important oil crop. Severe symptoms of the disease (e.g., plant dwarfism, leaf bleaching, sporulation and production of infertile flower) strongly impair seed yield. Pl resistance genes conferring resistance to specific P. halstedii pathotypes were located on sunflower genetic map but yet not cloned. They are present in cultivated lines to protect them against downy mildew disease. Among the 16 different P. halstedii pathotypes recorded in France, pathotype 710 is frequently found, and therefore continuously controlled in sunflower by different Pl genes. High-throughput sequencing of cDNA from P. halstedii led us to identify potential effectors with the characteristic RXLR or CRN motifs described in other oomycetes. Expression of six P. halstedii putative effectors, five RXLR and one CRN, was analyzed by qRT-PCR in pathogen spores and in the pathogen infecting sunflower leaves and selected for functional analyses. We developed a new method for transient expression in sunflower plant leaves and showed for the first time subcellular localization of P. halstedii effectors fused to a fluorescent protein in sunflower leaf cells. Overexpression of the CRN and of 3 RXLR effectors induced hypersensitive-like cell death reactions in some sunflower near-isogenic lines resistant to pathotype 710 and not in susceptible corresponding lines, suggesting they could be involved in Pl loci-mediated resistances.
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Affiliation(s)
- Quentin Gascuel
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Luis Buendia
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Yann Pecrix
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Nicolas Blanchet
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | | | - Laurence Godiard
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
- *Correspondence: Laurence Godiard,
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