1
|
Hassett K, Muria-Gonzalez MJ, Martin A, Karakaya A, Çelik Oğuz A, Bakonyi J, Knight NL, Prins R, Ellwood SR. Global Spread, Genetic Differentiation, and Selection of Barley Spot Form Net Blotch Isolates. PHYTOPATHOLOGY 2024; 114:1542-1553. [PMID: 38619562 DOI: 10.1094/phyto-11-23-0442-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Aziz Karakaya
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Arzu Çelik Oğuz
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Jószef Bakonyi
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó str. 15, 1022 Budapest, Hungary
| | - Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Renée Prins
- CenGen (Pty) Ltd., Worcester, 6850, South Africa
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| |
Collapse
|
2
|
Dorigan AF, Moreira SI, da Silva Costa Guimarães S, Cruz-Magalhães V, Alves E. Target and non-target site mechanisms of fungicide resistance and their implications for the management of crop pathogens. PEST MANAGEMENT SCIENCE 2023; 79:4731-4753. [PMID: 37592727 DOI: 10.1002/ps.7726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
Fungicides are indispensable for high-quality crops, but the rapid emergence and evolution of fungicide resistance have become the most important issues in modern agriculture. Hence, the sustainability and profitability of agricultural production have been challenged due to the limited number of fungicide chemical classes. Resistance to site-specific fungicides has principally been linked to target and non-target site mechanisms. These mechanisms change the structure or expression level, affecting fungicide efficacy and resulting in different and varying resistance levels. This review provides background information about fungicide resistance mechanisms and their implications for developing anti-resistance strategies in plant pathogens. Here, our purpose was to review changes at the target and non-target sites of quinone outside inhibitor (QoI) fungicides, methyl-benzimidazole carbamate (MBC) fungicides, demethylation inhibitor (DMI) fungicides, and succinate dehydrogenase inhibitor (SDHI) fungicides and to evaluate if they may also be associated with a fitness cost on crop pathogen populations. The current knowledge suggests that understanding fungicide resistance mechanisms can facilitate resistance monitoring and assist in developing anti-resistance strategies and new fungicide molecules to help solve this issue. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
| | | | | | | | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, Lavras, Brazil
| |
Collapse
|
3
|
Huang X, Wang X, Zhou L, Kong F, Liu Y, Wang Z, Zhang H. TaqMan-MGB PCR Method for Rapid Detection of QoI Fungicide Resistance in Chinese Populations of Plasmopara viticola. PLANT DISEASE 2023; 107:3007-3013. [PMID: 36856651 DOI: 10.1094/pdis-12-22-2954-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: 06/18/2023]
Abstract
Grape downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevine worldwide. Quinone outside inhibitor (QoI) fungicides are commonly used for the control of the pathogen in grape fields across China. However, their recurrent use could lead to the emergence of resistance against these compounds. Based on the most common mutation in resistant isolates, a glycine to alanine substitution at amino acid position 143 (G143A) in the cytochrome b protein, a TaqMan-MGB PCR was developed for the rapid detection of resistance to the QoI fungicide azoxystrobin in P. viticola. Specificity and sensitivity of this method showed it could specifically detect the point mutations linked with QoI resistance in P. viticola, and the detection limit was 0.2 pg. It could also quantify the resistance allele even in isolate mixtures containing as little as 5% QoI-resistant P. viticola strains. With this method, a large P. viticola population (n = 2,373) was screened, and QoI-resistant isolates were identified for the first time in China. The average frequencies of the resistant genotype from eight major-grapevine regions were up to 66%. Taken together, the results not only provide a novel tool for the rapid distinction and quantification of the QoI-resistant allele in P. viticola but also provide important references for fungicide selection and application, which will facilitate resistance management of grape downy mildew and improve grape production systems in Chinese vineyards.
Collapse
Affiliation(s)
- Xiaoqing Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xina Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Fanfang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Zhongyue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| |
Collapse
|
4
|
Wu PH, Chang HX, Shen YM. Effects of synthetic and environmentally friendly fungicides on powdery mildew management and the phyllosphere microbiome of cucumber. PLoS One 2023; 18:e0282809. [PMID: 36888572 PMCID: PMC9994715 DOI: 10.1371/journal.pone.0282809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Modern agricultural practices rely on synthetic fungicides to control plant disease, but the application of these fungicides has raised concerns regarding human and environmental health for many years. As a substitute, environmentally friendly fungicides have been increasingly introduced as alternatives to synthetic fungicides. However, the impact of these environmentally friendly fungicides on plant microbiomes has received limited attention. In this study, we used amplicon sequencing to compare the bacterial and fungal microbiomes in the leaves of powdery mildew-infected cucumber after the application of two environmentally friendly fungicides (neutralized phosphorous acid (NPA) and sulfur) and one synthetic fungicide (tebuconazole). The phyllosphere α-diversity of both the bacterial and fungal microbiomes showed no significant differences among the three fungicides. For phyllosphere β-diversity, the bacterial composition exhibited no significant differences among the three fungicides, but fungal composition was altered by the synthetic fungicide tebuconazole. While all three fungicides significantly reduced disease severity and the incidence of powdery mildew, NPA and sulfur had minimal impacts on the phyllosphere fungal microbiome relative to the untreated control. Tebuconazole altered the phyllosphere fungal microbiome by reducing the abundance of fungal OTUs such as Dothideomycetes and Sordariomycetes, which included potentially beneficial endophytic fungi. These results indicated that treatments with the environmentally friendly fungicides NPA and sulfur have fewer impacts on the phyllosphere fungal microbiome while maintaining the same control efficacy as the synthetic fungicide tebuconazole.
Collapse
Affiliation(s)
- Ping-Hu Wu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan
| | - Yuan-Min Shen
- Master Program for Plant Medicine, National Taiwan University, Taipei City, Taiwan
- * E-mail:
| |
Collapse
|
5
|
Dorigan AF, Moreira SI, Ceresini PC, Pozza EA, Belan LL, da Silveira PR, Alves E. Higher fitness and competitive advantage of Pyricularia oryzae Triticum lineage resistant to QoI fungicides. PEST MANAGEMENT SCIENCE 2022; 78:5251-5258. [PMID: 36054071 DOI: 10.1002/ps.7144] [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: 05/27/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Quinone outside inhibitor (QoI) fungicides have not been effective in controlling the wheat blast disease [Pyricularia oryzae Triticum lineage (PoTl)] in Brazil. The first report of resistance of PoTl to QoIs in this country occurred in 2015. This study aimed to test hypotheses about the changes in fitness parameters and competitive advantage of the QoI-resistant (R) PoTl isolate group compared to the sensitive (S) isolate group. Mycelial growth on PDA medium and in vivo conidial production, incubation period and disease severity were analyzed as fitness parameters. The competitive ability was measured on wheat leaves and heads inoculated with mixtures of R:S isolates at the following proportions: 0S:100R, 20S:80R, 50S:50R, 80S:20R, 100S:0R, and 0S:0R. RESULTS The QoI-R isolate group had significantly higher fitness than the sensitive isolate group, considering both in vitro and in vivo parameters. The highest in vivo conidial production on wheat leaves and the highest leaf and head disease severity were detected when resistant strains were predominant in the isolate's mixtures (20S:80R or 0S:100R proportions), in the absence of fungicide pressure. Conidia harvested from wheat blast lesions on leaves inoculated with 20S:80R and 0S:100R mixtures were resistant to QoIs in vitro assays based on discriminatory doses of the fungicide. CONCLUSION Therefore, QoI resistance facilitated a higher fitness and a competitive advantage in PoTl, which contrasts with the evolutionary theory that associates a fitness cost to fungicide resistance. We discuss the evolutionary and ecological implications of the higher fitness as found in the fungicide-resistant adapted populations of the wheat blast pathogen. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
| | | | - Paulo Cezar Ceresini
- Department of Crop Protection, Agricultural Engineering and Soils São Paulo State University, São Paulo, Brazil
| | | | - Leônidas Leoni Belan
- Center for Agricultural Sciences Campus Imperatriz, State University of Tocantina Region of Maranhão, São Luís, Brazil
| | | | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, Lavras, Brazil
| |
Collapse
|
6
|
Possamai T, Wiedemann-Merdinoglu S. Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine. FRONTIERS IN PLANT SCIENCE 2022; 13:930954. [PMID: 36035702 PMCID: PMC9403010 DOI: 10.3389/fpls.2022.930954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.
Collapse
Affiliation(s)
- Tyrone Possamai
- CREA—Research Centre for Viticulture and Enology, Conegliano, Italy
| | | |
Collapse
|
7
|
Noel ZA, Longley R, Benucci GMN, Trail F, Chilvers MI, Bonito G. Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management. ISME COMMUNICATIONS 2022; 2:19. [PMID: 36404932 PMCID: PMC9674006 DOI: 10.1038/s43705-022-00103-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.
Collapse
Affiliation(s)
- Zachary A. Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
- Present Address: Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849 USA
| | - Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
| | | | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
| |
Collapse
|
8
|
Deknock A, Pasmans F, van Leeuwenberg R, Van Praet S, Bruneel S, Lens L, Croubels S, Martel A, Goethals P. Alternative food sources interfere with removal of a fungal amphibian pathogen by zooplankton. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Arne Deknock
- Department of Animal Sciences and Aquatic Ecology Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Poultry Diseases Faculty of Veterinary Medicine Ghent University Merelbeke Belgium
| | - Robby van Leeuwenberg
- Department of Pathology, Bacteriology and Poultry Diseases Faculty of Veterinary Medicine Ghent University Merelbeke Belgium
| | - Sarah Van Praet
- Department of Pathology, Bacteriology and Poultry Diseases Faculty of Veterinary Medicine Ghent University Merelbeke Belgium
| | - Stijn Bruneel
- Department of Animal Sciences and Aquatic Ecology Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Luc Lens
- Department of Biology Faculty of Sciences Ghent University Ghent Belgium
| | - Siska Croubels
- Department of Pharmacology Toxicology and Biochemistry Faculty of Veterinary Medicine Ghent University Merelbeke Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Poultry Diseases Faculty of Veterinary Medicine Ghent University Merelbeke Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology Faculty of Bioscience Engineering Ghent University Ghent Belgium
| |
Collapse
|
9
|
Spanner R, Taliadoros D, Richards J, Rivera-Varas V, Neubauer J, Natwick M, Hamilton O, Vaghefi N, Pethybridge S, Secor GA, Friesen TL, Stukenbrock EH, Bolton MD. Genome-Wide Association and Selective Sweep Studies Reveal the Complex Genetic Architecture of DMI Fungicide Resistance in Cercospora beticola. Genome Biol Evol 2021; 13:6367780. [PMID: 34499119 DOI: 10.1093/gbe/evab209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 12/21/2022] Open
Abstract
The rapid and widespread evolution of fungicide resistance remains a challenge for crop disease management. The demethylation inhibitor (DMI) class of fungicides is a widely used chemistry for managing disease, but there has been a gradual decline in efficacy in many crop pathosystems. Reliance on DMI fungicides has increased resistance in populations of the plant pathogenic fungus Cercospora beticola worldwide. To better understand the genetic and evolutionary basis for DMI resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this species. We performed whole-genome resequencing of 190 C. beticola isolates infecting sugar beet (Beta vulgaris ssp. vulgaris). All isolates were phenotyped for sensitivity to the DMI tetraconazole. Intragenic markers on chromosomes 1, 4, and 9 were significantly associated with DMI fungicide resistance, including a polyketide synthase gene and the gene encoding the DMI target CbCYP51. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) and nonsynonymous mutations (L144F, I387M, and Y464S) associated with DMI resistance. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.
Collapse
Affiliation(s)
- Rebecca Spanner
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Demetris Taliadoros
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Christian-Albrechts University of Kiel, Germany
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Viviana Rivera-Varas
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Jonathan Neubauer
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Mari Natwick
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Olivia Hamilton
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Sarah Pethybridge
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Timothy L Friesen
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Eva H Stukenbrock
- Botanical Institute, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Melvin D Bolton
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| |
Collapse
|
10
|
Carisse O, Van der Heyden H, Tremblay DM, Hébert PO, Delmotte F. Evidence for Differences in the Temporal Progress of Plasmopara viticola Clades riparia and aestivalis Airborne Inoculum Monitored in Vineyards in Eastern Canada Using a Specific Multiplex Quantitative PCR Assay. PLANT DISEASE 2021; 105:1666-1676. [PMID: 33147122 DOI: 10.1094/pdis-06-20-1164-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Four clades of Plasmopara viticola isolated from wild and cultivated Vitis species were described in 2013. Only P. viticola clades riparia and aestivalis have been detected in eastern Canada. To increase our understanding of the epidemiology of these clades of P. viticola, airborne sporangia were monitored with spore samplers at two experimental vineyards from 2015 to 2018 and at 11, 14, and 15 commercial vineyards in 2016, 2017, and 2018, respectively. At each vineyard and in each year, airborne sporangia were assessed three times weekly from grapevine budbreak to harvest. To accurately monitor airborne inoculum, a specific and sensitive quantitative PCR assay for simultaneous quantification of P. viticola clades riparia and aestivalis was developed. At the experimental site, in the vineyard planted with the hybrid grape variety Chancellor, mostly P. viticola clade riparia was detected. In vineyards planted with multiple grape varieties, airborne sporangia of P. viticola clade riparia were prevalent at the beginning of the season, whereas P. viticola clade aestivalis was mostly detected from midseason to harvest. At the commercial sites, airborne sporangia of P. viticola clade riparia were more prevalent in 2016, whereas P. viticola clade aestivalis was more prevalent in 2017 and 2018. The only significant difference between the inoculum progress curves was the time at which 50% of the seasonal inoculum was reached, with an average for the 3 years of 100.8 and 117.9 days since 1 May for P. viticola clade riparia and clade aestivalis, respectively. When airborne sporangium concentrations were expressed as the proportion of the two clades, in general, the proportion of clade aestivalis to that of clade riparia was low at the beginning of the season and increased to reach approximately 0.9 to 1.0 at the end of the season. These results suggest that both clades of P. viticola coexist, but that clade aestivalis is predominant and that downy mildew epidemics caused by P. viticola clade riparia occur 2 to 3 weeks before those caused by clade aestivalis.
Collapse
Affiliation(s)
- O Carisse
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec J3B 3E6, Canada
| | - H Van der Heyden
- Compagnie de Recherche Phytodata Inc., Sherrington, Quebec J0L 2N0, Canada
| | - D M Tremblay
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec J3B 3E6, Canada
| | - P O Hébert
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec J3B 3E6, Canada
| | - F Delmotte
- Institut national de la recherche agronomique, Unité Mixe de Recherche 1065, Santé et Agroécologie du Vignoble, F-33883 Villenave d'Ornon, France
| |
Collapse
|
11
|
Liu R, Chen T, Yin X, Xiang G, Peng J, Fu Q, Li M, Shang B, Ma H, Liu G, Wang Y, Xu Y. A Plasmopara viticola RXLR effector targets a chloroplast protein PsbP to inhibit ROS production in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1557-1570. [PMID: 33783031 DOI: 10.1111/tpj.15252] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Pathogens secrete a large number of effectors that manipulate host processes to create an environment conducive to pathogen colonization. However, the underlying mechanisms by which Plasmopara viticola effectors manipulate host plant cells remain largely unclear. In this study, we reported that RXLR31154, a P. viticola RXLR effector, was highly expressed during the early stages of P. viticola infection. In our study, stable expression of RXLR31154 in grapevine (Vitis vinifera) and Nicotiana benthamiana promoted leaf colonization by P. viticola and Phytophthora capsici, respectively. By yeast two-hybrid screening, the 23-kDa oxygen-evolving enhancer 2 (VpOEE2 or VpPsbP), encoded by the PsbP gene, in Vitis piasezkii accession Liuba-8 was identified as a host target of RXLR31154. Overexpression of VpPsbP enhanced susceptibility to P. viticola in grapevine and P. capsici in N. benthamiana, and silencing of NbPsbPs, the homologs of PsbP in N. benthamiana, reduced P. capcisi colonization, indicating that PsbP is a susceptibility factor. RXLR31154 and VpPsbP protein were co-localized in the chloroplast. Moreover, VpPsbP reduced H2 O2 accumulation and activated the 1 O2 signaling pathway in grapevine. RXLR31154 could stabilize PsbP. Together, our data revealed that RXLR31154 reduces H2 O2 accumulation and activates the 1 O2 signaling pathway through stabilizing PsbP, thereby promoting disease.
Collapse
Affiliation(s)
- Ruiqi Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Tingting Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Xiao Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Gaoqing Xiang
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Jing Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Qingqing Fu
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Mengyuan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Boxing Shang
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Hui Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| |
Collapse
|
12
|
Peng Z, He Y, Parajuli S, You Q, Wang W, Bhattarai K, Palmateer AJ, Deng Z. Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens. HORTICULTURE RESEARCH 2021; 8:108. [PMID: 33931631 PMCID: PMC8087834 DOI: 10.1038/s41438-021-00543-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 05/11/2023]
Abstract
Downy mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant-pathogen interactions in the early stage of infection and quickly assess resistance/susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA-Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops.
Collapse
Affiliation(s)
- Ze Peng
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Yanhong He
- Visiting scholar at University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Saroj Parajuli
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Qian You
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Weining Wang
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Krishna Bhattarai
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Aaron J Palmateer
- University of Florida, IFAS, Department of Plant Pathology, Tropical Research and Education Center, 18905 S.W. 280th Street, Homestead, FL, 33031, USA
- Bayer Environmental Science US, 5000 Centregreen Way, Cary, NC, 27513, USA
| | - Zhanao Deng
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA.
| |
Collapse
|
13
|
Fontaine MC, Labbé F, Dussert Y, Delière L, Richart-Cervera S, Giraud T, Delmotte F. Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. Curr Biol 2021; 31:2155-2166.e4. [PMID: 33770491 DOI: 10.1016/j.cub.2021.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/04/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.
Collapse
Affiliation(s)
- Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France; Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France.
| | - Frédéric Labbé
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - Yann Dussert
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Sylvie Richart-Cervera
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - François Delmotte
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France.
| |
Collapse
|
14
|
Hawkins NJ, Fraaije BA. Contrasting levels of genetic predictability in the evolution of resistance to major classes of fungicides. Mol Ecol 2021; 30:5318-5327. [PMID: 33706414 DOI: 10.1111/mec.15877] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
The evolution of resistance has been seen across all major classes of xenobiotics, including antimicrobial drugs and agricultural pesticides. This repeated emergence of resistance is a case of phenotypic parallel evolution, but often the parallelism extends to the molecular level too, with multiple species gaining the same mutation in response to the same chemical treatment. We review the degree of repeatability in target-site resistance mutations affecting different classes of site-specific agricultural fungicides used in crop protection, comparing the extent to which resistance in different pathogen species has evolved via the same or different mutations. For all major fungicide target sites, substantial levels of molecular parallel evolution can be seen, with at least one mutation recurring in over 50% of species. Target-site mutations appear to be most repeatable in cytochrome b, target site of quinone-outside inhibitor fungicides, and least predictable for CYP51, target site of the azoles. Intermediate levels of repeatability are seen for the MBC target site β-tubulin, and the SDHI target site succinate dehydrogenase. Repeatability may be lower where there are selective trade-offs between resistance and pleiotropic fitness penalties, or differing levels of cross-resistance across members of a fungicide class; or where single mutations confer only partial resistance, and epistatic interactions between multiple mutations result in a rugged fitness landscape. This affects the predictive power of in vitro mutation studies, and has practical implications for resistance monitoring strategies and diagnostic methods.
Collapse
Affiliation(s)
- Nichola J Hawkins
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, UK.,NIAB, Cambridge, UK
| | | |
Collapse
|
15
|
Dunker F, Oberkofler L, Lederer B, Trutzenberg A, Weiberg A. An Arabidopsis downy mildew non-RxLR effector suppresses induced plant cell death to promote biotroph infection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:718-732. [PMID: 33063828 PMCID: PMC7853606 DOI: 10.1093/jxb/eraa472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 05/11/2023]
Abstract
Our understanding of obligate biotrophic pathogens is limited by lack of knowledge concerning the molecular function of virulence factors. We established Arabidopsis host-induced gene silencing (HIGS) to explore gene functions of Hyaloperonospora arabidopsidis, including CYSTEINE-RICH PROTEIN (HaCR)1, a potential secreted effector gene of this obligate biotrophic pathogen. HaCR1 HIGS resulted in H. arabidopsidis-induced local plant cell death and reduced pathogen reproduction. We functionally characterized HaCR1 by ectopic expression in Nicotiana benthamiana. HaCR1 was capable of inhibiting effector-triggered plant cell death. Consistent with this, HaCR1 expression in N. benthamiana led to stronger disease symptoms caused by the hemibiotrophic oomycete pathogen Phytophthora capsici, but reduced disease symptoms caused by the necrotrophic fungal pathogen Botrytis cinerea. Expressing HaCR1 in transgenic Arabidopsis confirmed higher susceptibility to H. arabidopsidis and to the bacterial hemibiotrophic pathogen Pseudomonas syringae. Increased H. arabidopsidis infection was in accordance with reduced PATHOGENESIS RELATED (PR)1 induction. Expression of full-length HaCR1 was required for its function, which was lost if the signal peptide was deleted, suggesting its site of action in the plant apoplast. This study provides phytopathological and molecular evidence for the importance of this widespread, but largely unexplored class of non-RxLR effectors in biotrophic oomycetes.
Collapse
Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Lorenz Oberkofler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Bernhard Lederer
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
16
|
Fungicide Resistance Evolution and Detection in Plant Pathogens: Plasmopara viticola as a Case Study. Microorganisms 2021; 9:microorganisms9010119. [PMID: 33419171 PMCID: PMC7825580 DOI: 10.3390/microorganisms9010119] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
The use of single-site fungicides to control plant pathogens in the agroecosystem can be associated with an increased selection of resistance. The evolution of resistance represents one of the biggest challenges in disease control. In vineyards, frequent applications of fungicides are carried out every season for multiple years. The agronomic risk of developing fungicide resistance is, therefore, high. Plasmopara viticola, the causal agent of grapevine downy mildew, is a high risk pathogen associated with the development of fungicide resistance. P. viticola has developed resistance to most of the fungicide classes used and constitutes one of the most important threats for grapevine production. The goals of this review are to describe fungicide resistance evolution in P. viticola populations and how to conduct proper monitoring activities. Different methods have been developed for phenotyping and genotyping P. viticola for fungicide resistance and the different phases of resistance evolution and life cycles of the pathogen are discussed, to provide a full monitoring toolkit to limit the spread of resistance. A detailed revision of the available tools will help in shaping and harmonizing the monitoring activities between countries and organizations.
Collapse
|
17
|
Uesugi R, Jouraku A, Sukonthabhirom Na Pattalung S, Hinomoto N, Kuwazaki S, Kanamori H, Katayose Y, Sonoda S. Origin, selection, and spread of diamide insecticide resistance allele in field populations of diamondback moth in east and southeast Asia. PEST MANAGEMENT SCIENCE 2021; 77:313-324. [PMID: 33411414 DOI: 10.1002/ps.6020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The investigation of molecular mechanisms and evolution of resistance to insecticides is an ongoing challenge, as researchers must provide guidance to manage the resistance to achieve sustainable production in agriculture. Predicting, monitoring, and managing insecticide resistance requires information on the origins, selection, and spread of resistance genes. The resistance of Plutella xylostella (L.) against diamide insecticides is becoming an increasingly severe problem in east and southeast Asia. In this study, the evolution of resistance was investigated using a resistance allele [ryanodine receptor (RyR); G4946E mutation] and its flanking regions, as well as mitochondrial cytochrome c oxidase subunit I (mtCOI). RESULTS The sequences of the flanking region of the G4946E and mtCOI suggested that the G4946E mutation has a key role in resistance. Furthermore, the G4946E mutation has multiple origins, and congenic resistant mutations have spread across east and southeast Asia, despite substantial geographical barriers. In addition, the susceptibility of field populations partially recovered during winter, based on the observed decrease in the G4946E (resistant allele) frequency. Finally, the resistance level indexed by the frequency of the E4946 allele was significantly lower in non-overwintering regions than in overwintering regions. CONCLUSION The information of the present study is useful to monitor resistance using molecular markers and to develop strategies to delay the evolution of diamide resistance.
Collapse
Affiliation(s)
- Ryuji Uesugi
- Division of Agro-Environment Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Iwate, Japan
| | - Akiya Jouraku
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | | | - Norihide Hinomoto
- Department of Applied Entomology and Zoology, Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Seigo Kuwazaki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Hiroyuki Kanamori
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Yuichi Katayose
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shoji Sonoda
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
| |
Collapse
|
18
|
Santos RF, Ciampi-Guillardi M, Fraaije BA, de Oliveira AA, Amorim L. The Climate-Driven Genetic Diversity Has a Higher Impact on the Population Structure of Plasmopara viticola Than the Production System or QoI Fungicide Sensitivity in Subtropical Brazil. Front Microbiol 2020; 11:575045. [PMID: 33042088 PMCID: PMC7528563 DOI: 10.3389/fmicb.2020.575045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Downy mildew, caused by Plasmopara viticola, is the main disease affecting vineyards in subtropical Brazil. Here, we collected 94 P. viticola isolates from four organic and conventional vineyards in the two main grape-growing states of Brazil to evaluate the sensitivity to the quinone outside inhibitor (QoI) azoxystrobin by pheno- and genotyping assays. The impact of location, production system and sensitivity to QoI fungicides on the population genetics and structure of P. viticola was determined using 10 microsatellite markers. Cytochrome b sequencing revealed that 28 and 100% of the isolates from vineyards under organic and conventional management carried the G143A mutation, respectively. The G143A mutation was associated with high levels of azoxystrobin resistance. Three out of the 94 isolates analyzed carried the M125I alteration, not previously described in P. viticola, which was associated with a five-fold reduction in azoxystrobin sensitivity compared to wild-type isolates. Haplotype network analysis based on cytochrome b gene sequences suggested that the Brazilian populations are more closely related to the European than the North American population. A total of six haplotypes were identified, with two of them carrying the G143A mutation. Microsatellite analysis revealed high allelic and genotypic variation among the four populations. Population differentiation analyses indicated that state of origin directly influences the population biology of P. viticola, while production system and QoI sensitivity have little effect. Great genetic diversity, sexual reproduction and high levels of admixture were observed in Rio Grande do Sul State. In contrast, populations in São Paulo State were dominated by a few clonal genotypes, and no admixed genotype was detected between the two genetic pools identified in the state. This study raises the hypothesis that winter weather conditions influence the overwinter survival strategy with profound effects in the population biology of P. viticola.
Collapse
Affiliation(s)
- Ricardo F Santos
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Bart A Fraaije
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Amanda A de Oliveira
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Lilian Amorim
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| |
Collapse
|
19
|
Dussert Y, Legrand L, Mazet ID, Couture C, Piron MC, Serre RF, Bouchez O, Mestre P, Toffolatti SL, Giraud T, Delmotte F. Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola. Curr Biol 2020; 30:3897-3907.e4. [PMID: 32795448 DOI: 10.1016/j.cub.2020.07.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 02/02/2023]
Abstract
Mating types are self-incompatibility systems that promote outcrossing in plants, fungi, and oomycetes. Mating-type genes have been widely studied in plants and fungi but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570-kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Functional studies will, however, be required to validate the function of these genes and find the actual determinants of mating type. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.
Collapse
Affiliation(s)
- Yann Dussert
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France.
| | - Ludovic Legrand
- LIPM, INRAE, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | - Isabelle D Mazet
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France
| | | | | | - Olivier Bouchez
- INRAE, US 1426 GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Pere Mestre
- SVQV, INRAE, Université de Strasbourg, F-68000 Colmar, France
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, AgroParisTech, Universite Paris-Saclay, 91400 Orsay, France
| | - François Delmotte
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France.
| |
Collapse
|
20
|
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: 1.3] [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.
Collapse
|
21
|
Taylor AS, Knaus BJ, Grünwald NJ, Burgess T. Population Genetic Structure and Cryptic Species of Plasmopara viticola in Australia. PHYTOPATHOLOGY 2019; 109:1975-1983. [PMID: 31215840 DOI: 10.1094/phyto-04-19-0146-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildew of grape caused by Plasmopara viticola is a global pathogen of economic importance to commercial viticulture. In contrast to populations in the northern hemisphere, few studies have investigated the population biology, genetic diversity, and origin of the pathogen in Australian production systems. DNA was extracted from 381 P. viticola samples from Vitis vinifera and alternate hosts collected via fresh and herbarium leaves from populations within Australia and Whatman FTA cards from North America, Brazil, and Uruguay. A total of 32 DNA samples were provided from a French population. The populations were genotyped using 16 polymorphic microsatellite markers. Representative samples from within Australia, Brazil, and Uruguay were also genotyped to determine which of the cryptic species (clades) within the P. viticola species complex were present. Our findings suggest the Australian and South American populations of P. viticola are more closely related to the European population than the North American population, the reported source of origin of the pathogen. The Western Australian population had similarities to the South Australian population, and the tight clustering of samples suggests a single introduction into Western Australia. P. viticola clade aestivalis was the only clade detected in Australian and South American populations. Analysis of the Western Australian population suggests that it is reproducing clonally, but additional research is required to determine the mechanism as to how this is occurring.
Collapse
Affiliation(s)
- Andrew S Taylor
- Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
- Department of Primary Industries and Regional Development, Bunbury, Western Australia 6230, Australia
| | - Brian J Knaus
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Treena Burgess
- Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| |
Collapse
|
22
|
He MH, Wang YP, Wu EJ, Shen LL, Yang LN, Wang T, Shang LP, Zhu W, Zhan J. Constraining Evolution of Alternaria alternata Resistance to a Demethylation Inhibitor (DMI) Fungicide Difenoconazole. Front Microbiol 2019; 10:1609. [PMID: 31354690 PMCID: PMC6636547 DOI: 10.3389/fmicb.2019.01609] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023] Open
Abstract
Evolution of fungicide resistance in plant pathogens is one of major concerns in sustainable plant disease management. In this study, the genetics and potential of developing resistance to a demethylation inhibitor (DMI) fungicide, difenoconazole, in the fungal pathogen Alternaria alternata was investigated using a comparative analysis of genetic variation in molecular (Single Sequence Repeats, SSR) and phenotypic (fungicide tolerance) markers. No difenoconazole resistance was found in the 215 A. alternata isolates sampled from seven different ecological zones in China despite the widespread use of the fungicide for more than 20 years. This result suggests that the risk of developing resistance to difenoconazole in A. alternata is low and we hypothesize that the low risk is likely caused by fitness penalties incurred by resistant mutants and the multiple mechanisms involving in developing resistance. Heritability and plasticity account for ∼24 and 3% of phenotypic variation, respectively, indicating that genetic adaptation by sequence variation plays a more important role in the evolution of difenoconazole resistance than physiological adaptation by altering gene expression. Constraining selection in the evolution of A. alternata resistance to difenoconazole was documented by different patterns of population differentiation and isolate-by-distance between SSR markers and difenoconazole tolerance. Though the risk of developing resistance is low, the findings of significant differences in difenoconazole tolerance among isolates and populations, and a skewing distribution toward higher tolerance suggests that a stepwise accumulation of tolerance to the fungicide might be occurring in the pathogen populations. As a consequence, dynamic management programs guided by evolutionary principles such as spatiotemporal rotations of fungicides with different modes of action are critical to prevent the continued accumulation of tolerance or the evolution of resistance to difenoconazole and other DMI fungicides.
Collapse
Affiliation(s)
- Meng-Han He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Ping Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - E-Jiao Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin-Lin Shen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Na Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tian Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Ping Shang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiasui Zhan
- Key Laboratory for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
23
|
Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019; 11:954-969. [PMID: 30847481 PMCID: PMC6660063 DOI: 10.1093/gbe/evz048] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
Collapse
Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
| | | |
Collapse
|
24
|
Frenken T, Agha R, Schmeller DS, van West P, Wolinska J. Biological Concepts for the Control of Aquatic Zoosporic Diseases. Trends Parasitol 2019; 35:571-582. [PMID: 31076352 DOI: 10.1016/j.pt.2019.04.003] [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: 02/28/2019] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 12/26/2022]
Abstract
Aquatic zoosporic diseases are threatening global biodiversity and ecosystem services, as well as economic activities. Current means of controlling zoosporic diseases are restricted primarily to chemical treatments, which are usually harmful or likely to be ineffective in the long term. Furthermore, some of these chemicals have been banned due to adverse effects. As a result, there is a need for alternative methods with minimal side-effects on the ecosystem or environment. Here, we integrate existing knowledge of three poorly interconnected areas of disease research - amphibian conservation, aquaculture, and plankton ecology - and arrange it into seven biological concepts to control zoosporic diseases. These strategies may be less harmful and more sustainable than chemical approaches. However, more research is needed before safe application is possible.
Collapse
Affiliation(s)
- Thijs Frenken
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
| | - Ramsy Agha
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dirk S Schmeller
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Pieter van West
- Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute of Biology, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
25
|
Derbyshire MC, Denton-Giles M, Hane JK, Chang S, Mousavi-Derazmahalleh M, Raffaele S, Buchwaldt L, Kamphuis LG. A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum. PLoS One 2019; 14:e0214201. [PMID: 30921376 PMCID: PMC6438532 DOI: 10.1371/journal.pone.0214201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/10/2019] [Indexed: 01/08/2023] Open
Abstract
The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.
Collapse
Affiliation(s)
- Mark Charles Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- * E-mail:
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Micro-organismes (LIPM), Université de Toulouse, INRA, Toulouse, France
| | - Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatchewan, Saskatoon, Canada
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| |
Collapse
|
26
|
Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019. [PMID: 30847481 DOI: 10.1101/350041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
Collapse
Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
| | | |
Collapse
|
27
|
Toffolatti SL, Russo G, Campia P, Bianco PA, Borsa P, Coatti M, Torriani SF, Sierotzki H. A time-course investigation of resistance to the carboxylic acid amide mandipropamid in field populations of Plasmopara viticola treated with anti-resistance strategies. PEST MANAGEMENT SCIENCE 2018; 74:2822-2834. [PMID: 29749019 DOI: 10.1002/ps.5072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Despite anti-resistance strategies being recommended to reduce selection pressure on insensitive strains, no information is available on fungal population dynamics following their application in real field conditions. In this study, the effects on Plasmopara viticola populations of two identical spray programs, differing only in including or not the carboxylic acid amide (CAA) mandipropamid in mixture and in alternation with an anti-resistance partner, were compared in terms of downy mildew control efficacy and mandipropamid sensitivity in two commercial vineyards for four seasons. RESULTS Both programs effectively and similarly protected grapevine from downy mildew, despite different starting sensitivity levels of the P. viticola populations. In the vineyard where resistant strains were initially present, the frequency of mutations associated with resistance (G1105S/V) fluctuated within seasons in both programs and a shift towards sensitivity occurred after 3 years of the mandipropamid-free program. Where sensitivity was initially present, no changes occurred in the mandipropamid-free program and resistant strains were selected in the mandipropamid program in high disease pressure conditions. CONCLUSION The anti-resistance strategy including mandipropamid in mixture showed a good field performance, but did not completely prevent an increase in the frequency of insensitive strains. This supports the need for appropriate planning to determine which mixtures should be used in the field. © 2018 Society of Chemical Industry.
Collapse
Affiliation(s)
- Silvia L Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | - Paola Campia
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Piero A Bianco
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | | | | | | |
Collapse
|
28
|
Giraud T, Koskella B, Laine AL. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Mol Ecol 2018; 26:1703-1710. [PMID: 28409900 DOI: 10.1111/mec.14091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/14/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| |
Collapse
|
29
|
Hawkins NJ, Fraaije BA. Fitness Penalties in the Evolution of Fungicide Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:339-360. [PMID: 29958074 DOI: 10.1146/annurev-phyto-080417-050012] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The evolution of resistance poses an ongoing threat to crop protection. Fungicide resistance provides a selective advantage under fungicide selection, but resistance-conferring mutations may also result in fitness penalties, resulting in an evolutionary trade-off. These penalties may result from the functional constraints of an evolving target site or from the resource allocation costs of overexpression or active transport. The extent to which such fitness penalties are present has important implications for resistance management strategies, determining whether resistance persists or declines between treatments, and for resistance risk assessments for new modes of action. Experimental results have proven variable, depending on factors such as temperature, nutrient status, osmotic or oxidative stress, and pathogen life-cycle stage. Functional genetics tools allow pathogen genetic background to be controlled, but this in turn raises the question of epistatic interactions. Combining fitness penalties under various conditions into a field-realistic scenario poses an important future challenge.
Collapse
Affiliation(s)
- N J Hawkins
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
| | - B A Fraaije
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
| |
Collapse
|
30
|
Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
31
|
|