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Kim DS, Li Y, Ahn HK, Woods-Tör A, Cevik V, Furzer OJ, Ma W, Tör M, Jones JDG. ATR2 C ala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition. THE NEW PHYTOLOGIST 2024; 243:330-344. [PMID: 38742296 DOI: 10.1111/nph.19790] [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: 03/11/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Arabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. ATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. Two additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2-recognizing accessions.
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Affiliation(s)
- Dae Sung Kim
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yufei Li
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Woods-Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Oliver J Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
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Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
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Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
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Hadimani S, De Britto S, Udayashankar AC, Geetha N, Nayaka CS, Ali D, Alarifi S, Ito SI, Jogaiah S. Genome-Wide Characterization of Effector Protein-Encoding Genes in Sclerospora graminicola and Its Validation in Response to Pearl Millet Downy Mildew Disease Stress. J Fungi (Basel) 2023; 9:jof9040431. [PMID: 37108886 PMCID: PMC10142805 DOI: 10.3390/jof9040431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the essential food crop for over ninety million people living in drier parts of India and South Africa. Pearl millet crop production is harshly hindered by numerous biotic stresses. Sclerospora graminicola causes downy mildew disease in pearl millet. Effectors are the proteins secreted by several fungi and bacteria that manipulate the host cell structure and function. This current study aims to identify genes encoding effector proteins from the S. graminicola genome and validate them through molecular techniques. In silico analyses were employed for candidate effector prediction. A total of 845 secretory transmembrane proteins were predicted, out of which 35 proteins carrying LxLFLAK (Leucine–any amino acid–Phenylalanine–Leucine–Alanine–Lysine) motif were crinkler, 52 RxLR (Arginine, any amino acid, Leucine, Arginine), and 17 RxLR-dEER putative effector proteins. Gene validation analysis of 17 RxLR-dEER effector protein-producing genes was carried out, of which 5genes were amplified on the gel. These novel gene sequences were submitted to NCBI. This study is the first report on the identification and characterization of effector genes in Sclerospora graminicola. This dataset will aid in the integration of effector classes that act independently, paving the way to investigate how pearl millet responds to effector protein interactions. These results will assist in identifying functional effector proteins involving the omic approach using newer bioinformatics tools to protect pearl millet plants against downy mildew stress. Considered together, the identified effector protein-encoding functional genes can be utilized in screening oomycetes downy mildew diseases in other crops across the globe.
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Affiliation(s)
- Shiva Hadimani
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India
| | - Savitha De Britto
- Division of Biological Sciences, School of Science and Technology, University of Goroka, Goroka 441, Papua New Guinea
| | - Arakere C. Udayashankar
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Nagaraj Geetha
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Chandra S. Nayaka
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shin-ichi Ito
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India
- Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periye (PO) 671316, Kasaragod (DT), Kerala, India
- Correspondence: ; Tel.: +91-836-2779533; Fax: +91-836-2747884
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Cottrell MT. A Search for Diastatic Enzymes Endogenous to Humulus lupulus and Produced by Microbes Associated with Pellet Hops Driving “Hop Creep” of Dry Hopped Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Stokholm A, Van Simaeys K, Gallagher A, Weaver G, Shellhammer TH. Investigating the Effect of Farm Management, Soil, and Climate on Hop Diastatic Potential. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1977902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Arnbjørn Stokholm
- Deptartment of Food Science and Technology, Oregon State University, Corvallis, OR, U.S.A
| | - Karli Van Simaeys
- Deptartment of Food Science and Technology, Oregon State University, Corvallis, OR, U.S.A
| | | | | | - Thomas H. Shellhammer
- Deptartment of Food Science and Technology, Oregon State University, Corvallis, OR, U.S.A
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Bello JC, Hausbeck MK, Sakalidis ML. Application of Target Enrichment Sequencing for Population Genetic Analyses of the Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli in Michigan. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1103-1118. [PMID: 34227836 DOI: 10.1094/mpmi-11-20-0329-ta] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Technological advances in genome sequencing have improved our ability to catalog genomic variation and have led to an expansion of the scope and scale of genetic studies over the past decade. Yet, for agronomically important plant pathogens such as the downy mildews (Peronosporaceae), the scale of genetic studies remains limited. This is, in part, due to the difficulties associated with maintaining obligate pathogens and the logistical constraints involved in the genotyping of these species (e.g., obtaining DNA of sufficient quantity and quality). To gain an evolutionary and ecological perspective of downy mildews, adaptable methods for the genotyping of their populations are required. Here, we describe a targeted enrichment (TE) protocol to genotype isolates from two Pseudoperonospora species (P. cubensis and P. humuli), using less than 50 ng of mixed pathogen and plant DNA for library preparation. We were able to enrich 830 target genes across 128 samples and identified 2,514 high-quality single nucleotide polymorphism (SNP) variants. Using these SNPs, we detected significant genetic differentiation (analysis of molecular variance [AMOVA], P = 0.01) between P. cubensis subpopulations from Cucurbita moschata (clade I) and Cucumis sativus (clade II) in the state of Michigan. No evidence of location-based differentiation was detected within the P. cubensis (clade II) subpopulation in Michigan. However, a significant effect of location on the genetic variation of the P. humuli subpopulation was detected in the state (AMOVA, P = 0.01). Mantel tests found evidence that the genetic distance among P. humuli samples was associated with the physical distance of the hop yards from which the samples were collected (P = 0.005). The differences in the distribution of genetic variation of the Michigan P. humuli and P. cubensis subpopulations suggest differences in the dispersal of these two species. The TE protocol described here provides an additional tool for genotyping obligate biotrophic plant pathogens and the execution of new genetic studies.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Julian C Bello
- Department of Plant, Soil and Microbial Sciences, Michigan State, University, East Lansing, MI 48824, U.S.A
| | - Mary K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State, University, East Lansing, MI 48824, U.S.A
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State, University, East Lansing, MI 48824, U.S.A
- Department of Forestry, Michigan State University, East Lansing, MI 48824, U.S.A
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Purayannur S, Gent DH, Miles TD, Radišek S, Quesada‐Ocampo LM. The hop downy mildew pathogen Pseudoperonospora humuli. MOLECULAR PLANT PATHOLOGY 2021; 22:755-768. [PMID: 33942461 PMCID: PMC8232024 DOI: 10.1111/mpp.13063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew, one of the most devastating diseases of cultivated hop, Humulus lupulus. Downy mildew occurs in all production areas of the crop in the Northern Hemisphere and Argentina. The pathogen overwinters in hop crowns and roots, and causes considerable crop loss. Downy mildew is managed by sanitation practices, planting of resistant cultivars, and fungicide applications. However, the scarcity of sources of host resistance and fungicide resistance in pathogen populations complicates disease management. This review summarizes the current knowledge on the symptoms of the disease, life cycle, virulence factors, and management of hop downy mildew, including various forecasting systems available in the world. Additionally, recent developments in genomics and effector discovery, and the future prospects of using such resources in successful disease management are also discussed. TAXONOMY Class: Oomycota; Order: Peronosporales; Family: Peronosporaceae; Genus: Pseudoperonospora; Species: Pseudoperonospora humuli. DISEASE SYMPTOMS The disease is characterized by systemically infected chlorotic shoots called "spikes". Leaf symptoms and signs include angular chlorotic lesions and profuse sporulation on the abaxial side of the leaf. Under severe disease pressure, dark brown discolouration or lesions are observed on cones. Infected crowns have brown to black streaks when cut open. Cultivars highly susceptible to crown rot may die at this phase of the disease cycle without producing shoots. However, foliar symptoms may not be present on plants with systemically infected root systems. INFECTION PROCESS Pathogen mycelium overwinters in buds and crowns, and emerges on infected shoots in spring. Profuse sporulation occurs on infected tissues and sporangia are released and dispersed by air currents. Under favourable conditions, sporangia germinate and produce biflagellate zoospores that infect healthy tissue, thus perpetuating the infection cycle. Though oospores are produced in infected tissues, their role in the infection cycle is not defined. CONTROL Downy mildew on hop is managed by a combination of sanitation practices and timely fungicide applications. Forecasting systems are used to time fungicide applications for successful management of the disease. USEFUL WEBSITES: https://content.ces.ncsu.edu/hop-downy-mildew (North Carolina State University disease factsheet), https://www.canr.msu.edu/resources/michigan-hop-management-guide (Michigan Hop Management Guide), http://uspest.org/risk/models (Oregon State University Integrated Plant Protection Center degree-day model for hop downy mildew), https://www.usahops.org/cabinet/data/Field-Guide.pdf (Field Guide for Integrated Pest Management in Hops).
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Affiliation(s)
- Savithri Purayannur
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - David H. Gent
- US Department of Agriculture‐Agricultural Research Service, Forage Seed and Cereal Research Unit, and Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Timothy D. Miles
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Sebastjan Radišek
- Plant Protection DepartmentDiagnostics LaboratorySlovenian Institute for Hop Research and BrewingŽalecSlovenia
| | - Lina M. Quesada‐Ocampo
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
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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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