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Kusch S, Frantzeskakis L, Lassen BD, Kümmel F, Pesch L, Barsoum M, Walden KD, Panstruga R. A fungal plant pathogen overcomes mlo-mediated broad-spectrum disease resistance by rapid gene loss. THE NEW PHYTOLOGIST 2024. [PMID: 39155769 DOI: 10.1111/nph.20063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps. Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad-spectrum resistance conditioned by barley loss-of-function mlo mutants. Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small-sized (c. 8-40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein-encoding genes that is absent in mlo-avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo-virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events. This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon-enriched genome.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Birthe D Lassen
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Mirna Barsoum
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Kim D Walden
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
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2
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Kusch S, Qian J, Loos A, Kümmel F, Spanu PD, Panstruga R. Long-term and rapid evolution in powdery mildew fungi. Mol Ecol 2024; 33:e16909. [PMID: 36862075 DOI: 10.1111/mec.16909] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Jiangzhao Qian
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Anne Loos
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Florian Kümmel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
- Imperial College, London, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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3
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Li Z, Velásquez‐Zapata V, Elmore JM, Li X, Xie W, Deb S, Tian X, Banerjee S, Jørgensen HJL, Pedersen C, Wise RP, Thordal‐Christensen H. Powdery mildew effectors AVR A1 and BEC1016 target the ER J-domain protein HvERdj3B required for immunity in barley. MOLECULAR PLANT PATHOLOGY 2024; 25:e13463. [PMID: 38695677 PMCID: PMC11064805 DOI: 10.1111/mpp.13463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024]
Abstract
The barley powdery mildew fungus, Blumeria hordei (Bh), secretes hundreds of candidate secreted effector proteins (CSEPs) to facilitate pathogen infection and colonization. One of these, CSEP0008, is directly recognized by the barley nucleotide-binding leucine-rich-repeat (NLR) receptor MLA1 and therefore is designated AVRA1. Here, we show that AVRA1 and the sequence-unrelated Bh effector BEC1016 (CSEP0491) suppress immunity in barley. We used yeast two-hybrid next-generation interaction screens (Y2H-NGIS), followed by binary Y2H and in planta protein-protein interactions studies, and identified a common barley target of AVRA1 and BEC1016, the endoplasmic reticulum (ER)-localized J-domain protein HvERdj3B. Silencing of this ER quality control (ERQC) protein increased Bh penetration. HvERdj3B is ER luminal, and we showed using split GFP that AVRA1 and BEC1016 translocate into the ER signal peptide-independently. Overexpression of the two effectors impeded trafficking of a vacuolar marker through the ER; silencing of HvERdj3B also exhibited this same cellular phenotype, coinciding with the effectors targeting this ERQC component. Together, these results suggest that the barley innate immunity, preventing Bh entry into epidermal cells, requires ERQC. Here, the J-domain protein HvERdj3B appears to be essential and can be regulated by AVRA1 and BEC1016. Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host NLR receptors. Previous work has shown that AVRA1 is directly recognized in the cytosol by the immune receptor MLA1. We speculate that the AVRA1 J-domain target being inside the ER, where it is inapproachable by NLRs, has forced the plant to evolve this challenging direct recognition.
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Affiliation(s)
- Zizhang Li
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Present address:
Institute for Bioscience and Biotechnology Research & Department of Plant Sciences and Landscape ArchitectureUniversity of MarylandRockvilleMarylandUSA
| | - Valeria Velásquez‐Zapata
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- Present address:
GreenLight Biosciences, IncResearch Triangle ParkNorth CarolinaUSA
| | - J. Mitch Elmore
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- USDA‐Agricultural Research Service, Corn Insects and Crop Genetics Research UnitAmesIowaUSA
- Present address:
USDA‐Agricultural Research Service, Cereal Disease LaboratorySt. PaulMinnesotaUSA
| | - Xuan Li
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Wenjun Xie
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Sohini Deb
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Xiao Tian
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Sagnik Banerjee
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of StatisticsIowa State UniversityAmesIowaUSA
- Present address:
Bristol Myers SquibbSan DiegoCaliforniaUSA
| | - Hans J. L. Jørgensen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Carsten Pedersen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Roger P. Wise
- Program in Bioinformatics & Computational BiologyIowa State UniversityAmesIowaUSA
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
- USDA‐Agricultural Research Service, Corn Insects and Crop Genetics Research UnitAmesIowaUSA
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4
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Xue P, Zhang L, Fan R, Li Y, Han X, Qi T, Zhao L, Yu D, Shen QH. HvMPK4 phosphorylates HvWRKY1 to enhance its suppression of barley immunity to powdery mildew fungus. J Genet Genomics 2024; 51:313-325. [PMID: 37225086 DOI: 10.1016/j.jgg.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades play important roles in disease resistance in model plant species. However, the functions of MAPK signaling pathways in crop disease resistance are largely unknown. Here we report the function of HvMKK1-HvMPK4-HvWRKY1 module in barley immune system. HvMPK4 is identified to play a negative role in barley immune response against Bgh, as virus-induced gene silencing of HvMPK4 results in enhanced disease resistance whilst stably overexpressing HvMPK4 leads to super-susceptibility to Bgh infection. Furthermore, the barley MAPK kinase HvMKK1 is found to specifically interact with HvMPK4, and the activated HvMKK1DD variant specifically phosphorylates HvMPK4 in vitro. Moreover, the transcription factor HvWRKY1 is identified to be a downstream target of HvMPK4 and phosphorylated by HvMPK4 in vitro in the presence of HvMKK1DD. Phosphorylation assay coupled with mutagenesis analyses identifies S122, T284, and S347 in HvWRKY1 as the major residues phosphorylated by HvMPK4. HvWRKY1 is phosphorylated in barley at the early stages of Bgh infection, which enhances its suppression on barley immunity likely due to enhanced DNA-binding and transcriptional repression activity. Our data suggest that the HvMKK1-HvMPK4 kinase pair acts upstream of HvWRKY1 to negatively regulate barley immunity against powdery mildew.
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Affiliation(s)
- Pengya Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Renchun Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyun Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Qi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifang Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deshui Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Brabham HJ, Gómez De La Cruz D, Were V, Shimizu M, Saitoh H, Hernández-Pinzón I, Green P, Lorang J, Fujisaki K, Sato K, Molnár I, Šimková H, Doležel J, Russell J, Taylor J, Smoker M, Gupta YK, Wolpert T, Talbot NJ, Terauchi R, Moscou MJ. Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae. THE PLANT CELL 2024; 36:447-470. [PMID: 37820736 PMCID: PMC10827324 DOI: 10.1093/plcell/koad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
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Affiliation(s)
- Helen J Brabham
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Diana Gómez De La Cruz
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Motoki Shimizu
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | | | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jennifer Lorang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Koki Fujisaki
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - James Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yogesh Kumar Gupta
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Tom Wolpert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 617-0001, Japan
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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6
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Contreras MP, Lüdke D, Pai H, Toghani A, Kamoun S. NLR receptors in plant immunity: making sense of the alphabet soup. EMBO Rep 2023; 24:e57495. [PMID: 37602936 PMCID: PMC10561179 DOI: 10.15252/embr.202357495] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Plants coordinately use cell-surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich-repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad-spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi-disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.
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Affiliation(s)
| | - Daniel Lüdke
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Hsuan Pai
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | | | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
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7
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Crean EE, Bilstein-Schloemer M, Maekawa T, Schulze-Lefert P, Saur IML. A dominant-negative avirulence effector of the barley powdery mildew fungus provides mechanistic insight into barley MLA immune receptor activation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5854-5869. [PMID: 37474129 PMCID: PMC10540733 DOI: 10.1093/jxb/erad285] [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: 01/16/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) recognize pathogen effectors to mediate plant disease resistance often involving host cell death. Effectors escape NLR recognition through polymorphisms, allowing the pathogen to proliferate on previously resistant host plants. The powdery mildew effector AVRA13-1 is recognized by the barley NLR MLA13 and activates host cell death. We demonstrate here that a virulent form of AVRA13, called AVRA13-V2, escapes MLA13 recognition by substituting a serine for a leucine residue at the C-terminus. Counterintuitively, this substitution in AVRA13-V2 resulted in an enhanced MLA13 association and prevented the detection of AVRA13-1 by MLA13. Therefore, AVRA13-V2 is a dominant-negative form of AVRA13 and has probably contributed to the breakdown of Mla13 resistance. Despite this dominant-negative activity, AVRA13-V2 failed to suppress host cell death mediated by the MLA13 autoactive MHD variant. Neither AVRA13-1 nor AVRA13-V2 interacted with the MLA13 autoactive variant, implying that the binding moiety in MLA13 that mediates association with AVRA13-1 is altered after receptor activation. We also show that mutations in the MLA13 coiled-coil domain, which were thought to impair Ca2+ channel activity and NLR function, instead resulted in MLA13 autoactive cell death. Our results constitute an important step to define intermediate receptor conformations during NLR activation.
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Affiliation(s)
- Emma E Crean
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
| | | | - Takaki Maekawa
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Department for Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Paul Schulze-Lefert
- Department for Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Isabel M L Saur
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
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8
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Tamborski J, Seong K, Liu F, Staskawicz BJ, Krasileva KV. Altering Specificity and Autoactivity of Plant Immune Receptors Sr33 and Sr50 Via a Rational Engineering Approach. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:434-446. [PMID: 36867580 PMCID: PMC10561695 DOI: 10.1094/mpmi-07-22-0154-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many resistance genes deployed against pathogens in crops are intracellular nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs). The ability to rationally engineer the specificity of NLRs will be crucial in the response to newly emerging crop diseases. Successful attempts to modify NLR recognition have been limited to untargeted approaches or depended on previously available structural information or knowledge of pathogen-effector targets. However, this information is not available for most NLR-effector pairs. Here, we demonstrate the precise prediction and subsequent transfer of residues involved in effector recognition between two closely related NLRs without their experimentally determined structure or detailed knowledge about their pathogen effector targets. By combining phylogenetics, allele diversity analysis, and structural modeling, we successfully predicted residues mediating interaction of Sr50 with its cognate effector AvrSr50 and transferred recognition specificity of Sr50 to the closely related NLR Sr33. We created synthetic versions of Sr33 that contain amino acids from Sr50, including Sr33syn, which gained the ability to recognize AvrSr50 with 12 amino-acid substitutions. Furthermore, we discovered that sites in the LRR domain needed to transfer recognition specificity to Sr33 also influence autoactivity in Sr50. Structural modeling suggests these residues interact with a part of the NB-ARC domain, which we named the NB-ARC latch, to possibly maintain the inactive state of the receptor. Our approach demonstrates rational modifications of NLRs, which could be useful to enhance existing elite crop germplasm. [Formula: see text] Copyright © 2023 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)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Furong Liu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Ksenia V. Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
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9
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Liang X, Ma Z, Ke Y, Wang J, Wang L, Qin B, Tang C, Liu M, Xian X, Yang Y, Wang M, Zhang Y. Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection. PLANT, CELL & ENVIRONMENT 2023; 46:2222-2237. [PMID: 36929646 DOI: 10.1111/pce.14585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 06/08/2023]
Abstract
As a perennial woody plant, the rubber tree (Hevea brasiliensis) must adapt to various environmental challenges through gene expression in multiple cell types. It is still unclear how genes in this species are expressed at the cellular level and the precise mechanisms by which cells respond transcriptionally to environmental stimuli, especially in the case of pathogen infection. Here, we characterized the transcriptomes in Hevea leaves during early powdery mildew infection using single-cell RNA sequencing. We identified 10 cell types and constructed the first single-cell atlas of Hevea leaves. Distinct gene expression patterns of the cell clusters were observed under powdery mildew infection, which was especially significant in the epidermal cells. Most of the genes involved in host-pathogen interactions in epidermal cells exhibited a pattern of dramatically increased expression with increasing pseudotime. Interestingly, we found that the HbCNL2 gene, encoding a nucleotide-binding leucine-rich repeat protein, positively modulated the defence of rubber leaves against powdery mildew. Overexpression of the HbCNL2 gene triggered a typical cell death phenotype in tobacco leaves and a higher level of reactive oxygen species in the protoplasts of Hevea leaves. The HbCNL2 protein was located in the cytomembrane and nucleus, and its leucine-rich repeat domain interacted with the histidine kinase-like ATPase domain of the molecular chaperone HbHSP90 in the nucleus. Collectively, our results provide the first observation of the cellular and molecular responses of Hevea leaves to biotrophic pathogen infection and can guide the identification of disease-resistance genes in this important tree species.
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Affiliation(s)
- Xiaoyu Liang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Zhan Ma
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yuhang Ke
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Jiali Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Lifeng Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bi Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chaorong Tang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Mingyang Liu
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Xuemei Xian
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Ye Yang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Meng Wang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
| | - Yu Zhang
- College of Tropical Crops, Sanya Nanfan Research Institute, College of Plant Protection, Hainan University, Haikou, China
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10
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Bonnamy M, Pinel-Galzi A, Gorgues L, Chalvon V, Hébrard E, Chéron S, Nguyen TH, Poulicard N, Sabot F, Pidon H, Champion A, Césari S, Kroj T, Albar L. Rapid evolution of an RNA virus to escape recognition by a rice nucleotide-binding and leucine-rich repeat domain immune receptor. THE NEW PHYTOLOGIST 2023; 237:900-913. [PMID: 36229931 DOI: 10.1111/nph.18532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underlying the extremely fast adaptation of the virus to its host. We found that the RYMV3 gene that protects rice against the virus codes for a nucleotide-binding and leucine-rich repeat domain immune receptor (NLRs) from the Mla-like clade of NLRs. RYMV3 detects the virus by forming a recognition complex with the viral coat protein (CP). The virus escapes efficiently from detection by mutations in its CP, some of which interfere with the formation of the recognition complex. This study establishes that NLRs also confer in monocotyledonous plants immunity to viruses, and reveals an unexpected functional diversity for NLRs of the Mla clade that were previously only known as fungal disease resistance proteins. In addition, it provides precise insight into the mechanisms by which viruses adapt to plant immunity and gives important knowledge for the development of sustainable resistance against viral diseases of cereals.
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Affiliation(s)
- Mélia Bonnamy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Agnès Pinel-Galzi
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Lucille Gorgues
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Sophie Chéron
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | | | - Nils Poulicard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - François Sabot
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
| | - Hélène Pidon
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, 06484, Quedlinburg, Germany
| | | | - Stella Césari
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Laurence Albar
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
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11
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Huang Z, Liu J, Lu X, Guo Y, Li Y, Liu Y, Zhang R, Xing L, Cao A. Identification and transfer of a new Pm21 haplotype with high genetic diversity and a special molecular resistance mechanism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:10. [PMID: 36658294 PMCID: PMC9852157 DOI: 10.1007/s00122-023-04251-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
A new functional Pm21 haplotype, Pm21(8#), was cloned from the new wheat-H. villosa translocation line T6VS(8#)·6DL, which confers the same strong resistance to powdery mildew through a different resistance mechanism. Broad-spectrum disease resistance genes are desirable in crop breeding for conferring stable, durable resistance in field production. Pm21(4#) is a gene introduced from wild Haynaldia villosa into wheat that confers broad-spectrum resistance to wheat powdery mildew and has been widely used in wheat production for approximately 30 years. The discovery and transfer of new functional haplotypes of Pm21 into wheat will expand its genetic diversity in production and avoid the breakdown of resistance conferred by a single gene on a large scale. Pm21(4#) previously found from T6VS(4#)·6AL has been cloned. In this study, a new wheat-H. villosa translocation, T6VS(8#)·6DL, was identified. A new functional Pm21 haplotype, designated Pm21(8#), was cloned and characterized. The genomic structures and the splicing patterns of Pm21(4#) and Pm21(8#) were different, and widespread sequence diversity was observed in the gene coding region and the promoter region. In the field, Pm21(8#) conferred resistance to Blumeria graminis f. sp. tritici (Bgt), similar to Pm21(4#), indicating that Pm21(8#) was also a resistance gene. However, Bgt development during the infection stage was obviously different between Pm21(4#)- and Pm21(8#)-containing materials under the microscopic observation. Pm21(4#) inhibited the formation of haustoria and the development of hyphae in the initial infection stage, while Pm21(8#) limited the growth of hyphae and inhibited the formation of conidiophores in the late infection stage. Therefore, Pm21(8#) is a new functional Pm21 haplotype that provides a new gene resource for wheat breeding.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315000 China
| | - Xiangqian Lu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yifei Guo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yueying Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
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12
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Liao W, Nielsen ME, Pedersen C, Xie W, Thordal-Christensen H. Barley endosomal MONENSIN SENSITIVITY1 is a target of the powdery mildew effector CSEP0162 and plays a role in plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:118-129. [PMID: 36227010 PMCID: PMC9786837 DOI: 10.1093/jxb/erac403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Encasements formed around haustoria and biotrophic hyphae as well as hypersensitive reaction (HR) cell death are essential plant immune responses to filamentous pathogens. In this study we examine the components that may contribute to the absence of these responses in susceptible barley attacked by the powdery mildew fungus. We find that the effector CSEP0162 from this pathogen targets plant MONENSIN SENSITIVITY1 (MON1), which is important for the fusion of multivesicular bodies to their target membranes. Overexpression of CSEP0162 and silencing of barley MON1 both inhibit encasement formation. We find that the Arabidopsis ecotype No-0 has resistance to powdery mildew, and that this is partially dependent on MON1. Surprisingly, we find the MON1-dependent resistance in No-0 not only includes an encasement response, but also an effective HR. Similarly, silencing of MON1 in barley also blocks Mla3-mediated HR-based powdery mildew resistance. Our results indicate that MON1 is a vital plant immunity component, and we speculate that the barley powdery mildew fungus introduces the effector CSEP0162 to target MON1 and hence reduce encasement formation and HR.
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Affiliation(s)
- Wenlin Liao
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mads E Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Wenjun Xie
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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13
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Velásquez-Zapata V, Elmore JM, Fuerst G, Wise RP. An interolog-based barley interactome as an integration framework for immune signaling. Genetics 2022; 221:iyac056. [PMID: 35435213 PMCID: PMC9157089 DOI: 10.1093/genetics/iyac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem-, and stripe rust. We used interolog inference to construct a barley protein interactome (Hordeum vulgare predicted interactome, HvInt) comprising 66,133 edges and 7,181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared with the experimentally validated Arabidopsis interactome of 11,253 proteins and 73,960 interactions, verifying that the 2 networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific "omics" datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant and susceptible subnetworks. The resulting differentially coexpressed (resistant - susceptible) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to mildew resistance locus a (Mla) through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli + nucleotide-binding domains and extended these to additional MLA alleles, orthologs, and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
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Affiliation(s)
- Valeria Velásquez-Zapata
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Gregory Fuerst
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Roger P Wise
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
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14
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Evolution of resistance (R) gene specificity. Essays Biochem 2022; 66:551-560. [PMID: 35612398 DOI: 10.1042/ebc20210077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
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15
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Chapman AVE, Elmore JM, McReynolds M, Walley JW, Wise RP. SGT1-Specific Domain Mutations Impair Interactions with the Barley MLA6 Immune Receptor in Association with Loss of NLR Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:274-289. [PMID: 34889653 DOI: 10.1094/mpmi-08-21-0217-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Mla (Mildew resistance locus a) of barley (Hordeum vulgare L.) is an effective model for cereal immunity against fungal pathogens. Like many resistance proteins, variants of the MLA coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) receptor often require the HRS complex (HSP90, RAR1, and SGT1) to function. However, functional analysis of Sgt1 has been particularly difficult, as deletions are often lethal. Recently, we identified rar3 (required for Mla6 resistance 3), an in-frame Sgt1ΔKL308-309 mutation in the SGT1-specific domain, that alters resistance conferred by MLA but without lethality. Here, we use autoactive MLA6 and recombinant yeast-two-hybrid strains with stably integrated HvRar1 and HvHsp90 to determine that this mutation weakens but does not entirely disrupt the interaction between SGT1 and MLA. This causes a concomitant reduction in MLA6 protein accumulation below the apparent threshold required for effective resistance. The ΔKL308-309 deletion had a lesser effect on intramolecular interactions than alanine or arginine substitutions, and MLA variants that display diminished interactions with SGT1 appear to be disproportionately affected by the SGT1ΔKL308-309 mutation. We hypothesize that those dimeric plant CC-NLRs that appear unaffected by Sgt1 silencing are those with the strongest intermolecular interactions with it. Combining our data with recent work in CC-NLRs, we propose a cyclical model of the MLA-HRS resistosome interactions.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Antony V E Chapman
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - J Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Maxwell McReynolds
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Justin W Walley
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, U.S.A
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16
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Leissing F, Reinstädler A, Thieron H, Panstruga R. Gene Gun-Mediated Transient Gene Expression for Functional Studies in Plant Immunity. Methods Mol Biol 2022; 2523:63-77. [PMID: 35759191 DOI: 10.1007/978-1-0716-2449-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
One major threat to plant cultivation are fungal pathogens, which can cause substantial yield losses in agriculture. As an example, cereal powdery mildew fungi such as the barley (Hordeum vulgare) pathogen, Blumeria graminis f. sp. hordei (Bgh), are among the ten most relevant fungal plant pathogens in molecular plant pathology and can lead to yield losses of up to 30%. Plant Mildew resistance Locus O (MLO) genes are required for successful colonization of plants by powdery mildew fungi. Accordingly, loss-of-function mlo mutants confer durable resistance against powdery mildew fungi in many plant species. In the case of barley, mlo-based resistance has been used for more than 40 years in agriculture without powdery mildew fungi effectively overcoming this kind of immunity. However, the molecular basis of mlo resistance and function(s) of the transmembrane Mlo protein(s) are still incompletely understood. The generation of transgenic barley plants to study the plant immune response and the involvement of Mlo therein is time-consuming and challenging. Therefore, transient gene expression via gene gun-mediated particle bombardment became a popular, easy, and efficient tool to investigate different aspects of plant defense responses in barley. Since Bgh fails to penetrate leaf epidermal cells of mlo mutants, single-cell complementation upon biolistic transformation resulting in (over-)expression of Mlo can be used to characterize the Mlo protein functionally in vivo. In this chapter, we describe in detail the gene gun-mediated transient expression of Mlo in barley leaf epidermal cells followed by powdery mildew inoculation and the subsequent microscopic evaluation. However, gene gun-mediated transient gene expression may be also used to address other research questions or to transform the epidermal tissues of other plant organs and/or species.
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Affiliation(s)
- Franz Leissing
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Aachen, Germany
| | - Anja Reinstädler
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Aachen, Germany
| | - Hannah Thieron
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Aachen, Germany
| | - Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Aachen, Germany.
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17
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Bettgenhaeuser J, Hernández-Pinzón I, Dawson AM, Gardiner M, Green P, Taylor J, Smoker M, Ferguson JN, Emmrich P, Hubbard A, Bayles R, Waugh R, Steffenson BJ, Wulff BBH, Dreiseitl A, Ward ER, Moscou MJ. The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics. Nat Commun 2021; 12:6915. [PMID: 34824299 PMCID: PMC8617247 DOI: 10.1038/s41467-021-27288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Crop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes, Rps6, Rps7, and Rps8, contribute to immunity in barley to wheat stripe rust. Rps7 cosegregates with barley powdery mildew resistance at the Mla locus. Using transgenic complementation of different Mla alleles, we confirm allele-specific recognition of wheat stripe rust by Mla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.
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Affiliation(s)
- Jan Bettgenhaeuser
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | | | - Andrew M Dawson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Matthew Gardiner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - John N Ferguson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Peter Emmrich
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amelia Hubbard
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, England, UK
| | - Rosemary Bayles
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, England, UK
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brande B H Wulff
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Antonín Dreiseitl
- Department of Integrated Plant Protection, Agrotest Fyto Ltd, Havlíčkova 2787, CZ-767 01, Kroměříž, Czech Republic
| | - Eric R Ward
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- AgBiome, Research Triangle Park, NC, 27709, USA
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK.
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18
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Chapman AVE, Hunt M, Surana P, Velásquez-Zapata V, Xu W, Fuerst G, Wise RP. Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1. Genetics 2021; 217:6043926. [PMID: 33724411 DOI: 10.1093/genetics/iyaa026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/04/2020] [Indexed: 01/22/2023] Open
Abstract
Barley (Hordeum vulgare L.) Mla (Mildew resistance locus a) and its nucleotide-binding, leucine-rich-repeat receptor (NLR) orthologs protect many cereal crops from diseases caused by fungal pathogens. However, large segments of the Mla pathway and its mechanisms remain unknown. To further characterize the molecular interactions required for NLR-based immunity, we used fast-neutron mutagenesis to screen for plants compromised in MLA-mediated response to the powdery mildew fungus, Blumeria graminis f. sp. hordei. One variant, m11526, contained a novel mutation, designated rar3 (required for Mla6 resistance3), that abolishes race-specific resistance conditioned by the Mla6, Mla7, and Mla12 alleles, but does not compromise immunity mediated by Mla1, Mla9, Mla10, and Mla13. This is analogous to, but unique from, the differential requirement of Mla alleles for the co-chaperone Rar1 (required for Mla12 resistance1). We used bulked-segregant-exome capture and fine mapping to delineate the causal mutation to an in-frame Lys-Leu deletion within the SGS domain of SGT1 (Suppressor of G-two allele of Skp1, Sgt1ΔKL308-309), the structural region that interacts with MLA proteins. In nature, mutations to Sgt1 usually cause lethal phenotypes, but here we pinpoint a unique modification that delineates its requirement for some disease resistances, while unaffecting others as well as normal cell processes. Moreover, the data indicate that the requirement of SGT1 for resistance signaling by NLRs can be delimited to single sites on the protein. Further study could distinguish the regions by which pathogen effectors and host proteins interact with SGT1, facilitating precise editing of effector incompatible variants.
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Affiliation(s)
- Antony V E Chapman
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Matthew Hunt
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Priyanka Surana
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.,Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Valeria Velásquez-Zapata
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.,Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Weihui Xu
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Greg Fuerst
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.,Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA.,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
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19
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Yaeno T, Wahara M, Nagano M, Wanezaki H, Toda H, Inoue H, Eishima A, Nishiguchi M, Hisano H, Kobayashi K, Sato K, Yamaoka N. RACE1, a Japanese Blumeria graminis f. sp. hordei isolate, is capable of overcoming partially mlo-mediated penetration resistance in barley in an allele-specific manner. PLoS One 2021; 16:e0256574. [PMID: 34424930 PMCID: PMC8382181 DOI: 10.1371/journal.pone.0256574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Loss-of-function mutation of the MILDEW RESISTANCE LOCUS O (Mlo) gene confers durable and broad-spectrum resistance to powdery mildew fungi in various plants, including barley. In combination with the intracellular nucleotide-binding domain and leucine-rich repeat receptor (NLR) genes, which confer the race-specific resistance, the mlo alleles have long been used in barley breeding as genetic resources that confer robust non-race-specific resistance. However, a Japanese Blumeria graminis f. sp. hordei isolate, RACE1, has been reported to have the potential to overcome partially the mlo-mediated penetration resistance, although this is yet uncertain because the putative effects of NLR genes in the tested accessions have not been ruled out. In this study, we examined the reproducibility of the earlier report and found that the infectious ability of RACE1, which partially overcomes the mlo-mediated resistance, is only exerted in the absence of NLR genes recognizing RACE1. Furthermore, using the transient-induced gene silencing technique, we demonstrated that RACE1 can partially overcome the resistance in the host cells with suppressed MLO expression but not in plants possessing the null mutant allele mlo-5.
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Affiliation(s)
- Takashi Yaeno
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
- Research Unit for Citromics, Ehime University, Tarumi, Matsuyama, Ehime, Japan
| | - Miki Wahara
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | - Mai Nagano
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | - Hikaru Wanezaki
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | - Hirotaka Toda
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | - Hiroshi Inoue
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | - Ayaka Eishima
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
| | | | - Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Okayama, Japan
| | - Kappei Kobayashi
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
- Research Unit for Citromics, Ehime University, Tarumi, Matsuyama, Ehime, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Okayama, Japan
| | - Naoto Yamaoka
- Department of Agriculture, Ehime University, Tarumi, Matsuyama, Japan
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20
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Sánchez-Martín J, Keller B. NLR immune receptors and diverse types of non-NLR proteins control race-specific resistance in Triticeae. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102053. [PMID: 34052730 DOI: 10.1016/j.pbi.2021.102053] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Recent progress in large-scale sequencing, genomics, and rapid gene isolation techniques has accelerated the identification of race-specific resistance (R) genes and their corresponding avirulence (Avr) genes in wheat, barley, rye, and their wild relatives. Here, we describe the growing repertoire of identified R and Avr genes with special emphasis on novel R gene architectures, revealing that there is a large diversity of proteins encoded by race-specific resistance genes that extends beyond the canonical nucleotide-binding domain leucine-rich repeat proteins. Immune receptors with unique domain architectures controlling race-specific resistance possibly reveal novel aspects on the biology of host-pathogen interactions. We conclude that the polyploid cereal genomes have a large evolutionary potential to generate diverse types of resistance genes.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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21
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CEM, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:e66961. [PMID: 34288868 PMCID: PMC8294853 DOI: 10.7554/elife.66961] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Clare EM Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CentreIwateJapan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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22
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CE, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:66961. [PMID: 34288868 DOI: 10.1101/2021.01.26.428286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 05/21/2023] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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23
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Li Q, Jiang XM, Shao ZQ. Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley. Front Genet 2021; 12:694682. [PMID: 34108996 PMCID: PMC8181414 DOI: 10.3389/fgene.2021.694682] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023] Open
Abstract
Barley is one of the top 10 crop plants in the world. During its whole lifespan, barley is frequently infected by various pathogens. In this study, we performed genome-wide analysis of the largest group of plant disease resistance (R) genes, the nucleotide binding site-leucine-rich repeat receptor (NLR) gene, in an updated barley genome. A total of 468 NLR genes were identified from the improved barley genome, including one RNL subclass and 467 CNL subclass genes. Proteins of 43 barley CNL genes were shown to contain 25 different integrated domains, including WRKY and BED. The NLR gene number identified in this study is much larger than previously reported results in earlier versions of barley genomes, and only slightly fewer than that in the diploid wheat Triticum urartu. Barley Chromosome 7 contains the largest number of 112 NLR genes, which equals to seven times of the number of NLR genes on Chromosome 4. The majority of NLR genes (68%) are located in multigene clusters. Phylogenetic analysis revealed that at least 18 ancestral CNL lineages were presented in the common ancestor of barley, T. urartu and Arabidopsis thaliana. Among them fifteen lineages expanded to 533 sub-lineages prior to the divergence of barley and T. urartu. The barley genome inherited 356 of these sub-lineages and duplicated to the 467 CNL genes detected in this study. Overall, our study provides an updated profile of barley NLR genes, which should serve as a fundamental resource for functional gene mining and molecular breeding of barley.
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Affiliation(s)
| | | | - Zhu-Qing Shao
- School of Life Sciences, Nanjing University, Nanjing, China
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24
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Manser B, Koller T, Praz CR, Roulin AC, Zbinden H, Arora S, Steuernagel B, Wulff BBH, Keller B, Sánchez-Martín J. Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:993-1007. [PMID: 33629439 DOI: 10.1111/tpj.15214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 05/23/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) act as intracellular sensors for pathogen-derived effector proteins and trigger an immune response, frequently resulting in the hypersensitive cell death response (HR) of the infected host cell. The wheat (Triticum aestivum) NLR Pm2 confers resistance against the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) if the isolate contains the specific RNase-like effector AvrPm2. We identified and isolated seven new Pm2 alleles (Pm2e-i) in the wheat D-genome ancestor Aegilops tauschii and two new natural AvrPm2 haplotypes from Bgt. Upon transient co-expression in Nicotiana benthamiana, we observed a variant-specific HR of the Pm2 variants Pm2a and Pm2i towards AvrPm2 or its homolog from the AvrPm2 effector family, BgtE-5843, respectively. Through the introduction of naturally occurring non-synonymous single nucleotide polymorphisms and structure-guided mutations, we identified single amino acids in both the wheat NLR Pm2 and the fungal effector proteins AvrPm2 and BgtE-5843 responsible for the variant-specific HR of the Pm2 variants. Exchanging these amino acids led to a modified HR of the Pm2-AvrPm2 interaction and allowed the identification of the effector head epitope, a 20-amino-acid long unit of AvrPm2 involved in the HR. Swapping of the AvrPm2 head epitope to the non-HR-triggering AvrPm2 family member BgtE-5846 led to gain of a HR by Pm2a. Our study presents a molecular approach to identify crucial effector surface structures involved in the HR and demonstrates that natural and induced diversity in an immune receptor and its corresponding effectors can provide the basis for understanding and modifying NLR-effector specificity.
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Affiliation(s)
- Beatrice Manser
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Teresa Koller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
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25
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Velásquez-Zapata V, Elmore JM, Banerjee S, Dorman KS, Wise RP. Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PLoS Comput Biol 2021; 17:e1008890. [PMID: 33798202 PMCID: PMC8046355 DOI: 10.1371/journal.pcbi.1008890] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/14/2021] [Accepted: 03/17/2021] [Indexed: 12/21/2022] Open
Abstract
Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.
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Affiliation(s)
- Valeria Velásquez-Zapata
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - J. Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, United States of America
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, Iowa, United States of America
| | - Sagnik Banerjee
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Karin S. Dorman
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Roger P. Wise
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, United States of America
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, Iowa, United States of America
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26
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Wang Z, Huang J, Nie L, Hu Y, Zhang N, Guo Q, Guo J, Du B, Zhu L, He G, Chen R. Molecular and functional analysis of a brown planthopper resistance protein with two nucleotide-binding site domains. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2657-2671. [PMID: 33345280 DOI: 10.1093/jxb/eraa586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/15/2020] [Indexed: 05/26/2023]
Abstract
The brown planthopper (Nilaparvata lugens Stål, BPH) resistance gene BPH9 encodes an unusual coiled-coil (CC) nucleotide-binding leucine-rich repeat (LRR) protein with two nucleotide-binding site (NBS) domains. To understand how this CC-NBS-NBS-LRR (CNNL) protein regulates defense signaling and BPH resistance, we dissected each domain's functions. The CC domain of BPH9 self-associated and was sufficient to induce cell death. The region of 97-115 residues in the CC domain is crucial for self-association and activation. NBS2, which contains a complete set of NBS function motifs and inhibits CC domain activation, rather than NBS1, acts as a molecular switch to regulate the activity of BPH9. We demonstrated that the CC domain, the NBS domain, and the LRR domain of BPH9 associate with each other and themselves in planta. Further domain swapping experiments revealed that the CC domains of BPH9 and susceptible alleles were similarly competent to induce resistance and the hypersensitive response, while the LRR domain of BPH9 confers resistance specificity to BPH. These findings provide new insights into the regulatory mechanisms governing the activity of CNNL proteins.
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Affiliation(s)
- Zhizheng Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jin Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lingyun Nie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinxia Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ning Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qin Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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27
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Bauer S, Yu D, Lawson AW, Saur IML, Frantzeskakis L, Kracher B, Logemann E, Chai J, Maekawa T, Schulze-Lefert P. The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold. PLoS Pathog 2021; 17:e1009223. [PMID: 33534797 PMCID: PMC7857584 DOI: 10.1371/journal.ppat.1009223] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22, which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVRA6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVRA1, AVRA7, AVRA10/AVRA22, and AVRA13, suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVRA1 and AVRA6 as well as allelic AVRA10 and AVRA22 is largely determined by the receptors' C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVRA10 and five specific AVRA22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVRA effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.
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Affiliation(s)
- Saskia Bauer
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dongli Yu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aaron W. Lawson
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Isabel M. L. Saur
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Elke Logemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Takaki Maekawa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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28
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Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, Stam R, van Oosterhout C, Fairhead S, Heal R, Cocker JM, Bhanvadia S, Barrett W, Wu CH, Adachi H, Song T, Kamoun S, Vleeshouwers VGAA, Tomlinson L, Wulff BBH, Jones JDG. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. NATURE PLANTS 2021; 7:198-208. [PMID: 33574576 PMCID: PMC7116783 DOI: 10.1038/s41477-021-00854-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Affiliation(s)
- Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- US Department of Agriculture-Agricultural Research Service, Madison, WI, USA
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Bayer Crop Science, Chesterfield, MO, USA
| | - Agnieszka I Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Remco Stam
- Phytopathology, Technical University Munich, Freising, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan M Cocker
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- University of Hull, Hull, UK
| | - Shivani Bhanvadia
- Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
| | - William Barrett
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Saur IML, Hückelhoven R. Recognition and defence of plant-infecting fungal pathogens. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153324. [PMID: 33249386 DOI: 10.1016/j.jplph.2020.153324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Attempted infections of plants with fungi result in diverse outcomes ranging from symptom-less resistance to severe disease and even death of infected plants. The deleterious effect on crop yield have led to intense focus on the cellular and molecular mechanisms that explain the difference between resistance and susceptibility. This research has uncovered plant resistance or susceptibility genes that explain either dominant or recessive inheritance of plant resistance with many of them coding for receptors that recognize pathogen invasion. Approaches based on cell biology and phytochemistry have contributed to identifying factors that halt an invading fungal pathogen from further invasion into or between plant cells. Plant chemical defence compounds, antifungal proteins and structural reinforcement of cell walls appear to slow down fungal growth or even prevent fungal penetration in resistant plants. Additionally, the hypersensitive response, in which a few cells undergo a strong local immune reaction, including programmed cell death at the site of infection, stops in particular biotrophic fungi from spreading into surrounding tissue. In this review, we give a general overview of plant recognition and defence of fungal parasites tracing back to the early 20th century with a special focus on Triticeae and on the progress that was made in the last 30 years.
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Affiliation(s)
- Isabel M L Saur
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Ramann-Straße 2, 85354 Freising, Germany.
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Novakazi F, Krusell L, Jensen JD, Orabi J, Jahoor A, Bengtsson T. You Had Me at "MAGIC"!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew. Genes (Basel) 2020; 11:genes11121512. [PMID: 33352820 PMCID: PMC7766815 DOI: 10.3390/genes11121512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 11/23/2022] Open
Abstract
Blumeria graminis f. sp. hordei (Bgh), the causal agent of barley powdery mildew (PM), is one of the most important barley leaf diseases and is prevalent in most barley growing regions. Infection decreases grain quality and yields on average by 30%. Multi-parent advanced generation inter-cross (MAGIC) populations combine the advantages of bi-parental and association panels and offer the opportunity to incorporate exotic alleles into adapted material. Here, four barley MAGIC populations consisting of six to eight founders were tested for PM resistance in field trials in Denmark. Principle component and STRUCTURE analysis showed the populations were unstructured and genome-wide linkage disequilibrium (LD) decay varied between 14 and 38 Mbp. Genome-wide association studies (GWAS) identified 11 regions associated with PM resistance located on chromosomes 1H, 2H, 3H, 4H, 5H and 7H, of which three regions are putatively novel resistance quantitative trait locus/loci (QTL). For all regions high-confidence candidate genes were identified that are predicted to be involved in pathogen defense. Haplotype analysis of the significant SNPs revealed new allele combinations not present in the founders and associated with high resistance levels.
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Affiliation(s)
- Fluturë Novakazi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
| | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700 Horsens, Denmark;
| | - Jens Due Jensen
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Jihad Orabi
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Ahmed Jahoor
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
- Correspondence:
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31
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NOD-like receptor-mediated plant immunity: from structure to cell death. Nat Rev Immunol 2020; 21:305-318. [PMID: 33293618 DOI: 10.1038/s41577-020-00473-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 12/25/2022]
Abstract
Animal and plant immune systems use intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) to detect pathogens, resulting in the activation of immune responses that are often associated with localized host cell death. Whereas vertebrate NLRs detect evolutionarily conserved molecular patterns and have undergone comparatively little copy number expansion, plant NLRs detect virulence factors that have often diversified in plant pathogen populations, and thus plant NLRs have been subject to parallel diversification. Plant NLRs sense the presence of virulence factors with enzymatic virulence activity often indirectly through their modification of host target proteins. By contrast, phytopathogenic virulence factors without enzymatic activity are usually recognized by NLRs directly by their structure. Structural and biochemical analyses have shown that both indirect and direct recognition of plant pathogens trigger the oligomerization of plant NLRs into active complexes. Assembly into three-layered ring-like structures has emerged as a common principle of NLR activation in plants and animals, but with distinct amino-terminal domains initiating different signalling pathways. Collectively, these analyses point to host cell membranes as a convergence point for activated plant NLRs and the disruption of cellular ion homeostasis as a possible major factor in NLR-triggered cell death signalling.
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32
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Xu Y, Magwanga RO, Jin D, Cai X, Hou Y, Juyun Z, Agong SG, Wang K, Liu F, Zhou Z. Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton. BMC PLANT BIOLOGY 2020; 20:518. [PMID: 33183239 PMCID: PMC7664088 DOI: 10.1186/s12870-020-02726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/31/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. RESULTS A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180-55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5-17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What's more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. CONCLUSION Our study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.
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Affiliation(s)
- Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 40070 China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Dingsha Jin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zheng Juyun
- Economic Crops Research Institute of Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang province China
| | - Stephen Gaya Agong
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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Lindner S, Keller B, Singh SP, Hasenkamp Z, Jung E, Müller MC, Bourras S, Keller B. Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:200-214. [PMID: 32645755 DOI: 10.1111/tpj.14917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The development of improved plant nucleotide-binding, leucine-rich repeat (LRR) immune receptors (NLRs) has mostly been based on random mutagenesis or on structural information available for specific receptors complexed with the recognized pathogen effector. Here, we use a targeted mutagenesis approach based on the natural diversity of the Pm3 powdery mildew resistance alleles present in different wheat (Triticum aestivum) genotypes. In order to understand the functional importance of the amino acid polymorphisms between the active immune receptor PM3A and the inactive ancestral variant PM3CS, we exchanged polymorphic regions and residues in the LRR domain of PM3A with the corresponding segments of PM3CS. These novel variants were functionally tested for recognition of the corresponding AVRPM3A2/F2 avirulence protein in Nicotiana benthamiana. We identified polymorphic residues in four regions of PM3A that enhance the immune response, but also residues that reduce it or result in complete loss of function. We found that the identified critical residues in PM3A modify its activation threshold towards different protein variants of AVRPM3A2/F2 . PM3A variants with a lowered threshold gave a stronger overall response and gained an extended recognition spectrum. One of these variant proteins with a single amino acid change was stably transformed into wheat, where it conferred race-specific resistance to mildew. This is a proof of concept that improved PM3A variants with an enlarged recognition spectrum can be engineered based on natural diversity by exchanging single or multiple residues that modulate resistance function.
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Affiliation(s)
- Stefan Lindner
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Bettina Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Simrat P Singh
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Zsuzsanna Hasenkamp
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Marion C Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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Lee RR, Chae E. Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes. PLANT COMMUNICATIONS 2020; 1:100089. [PMID: 33367252 PMCID: PMC7747988 DOI: 10.1016/j.xplc.2020.100089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 05/04/2023]
Abstract
The nucleotide-binding domain and leucine-rich repeat (NLR) gene family is highly expanded in the plant lineage with extensive sequence and structure polymorphisms. To survey the landscape of NLR expansion, we mined the published long-read data generated by the resistance gene enrichment sequencing of 64 diverse Arabidopsis thaliana accessions. We found that the hot spots of massive multi-gene NLR cluster expansion did not typically span the whole cluster; instead, they were restricted to a handful of, or only one, dominant radiation(s). All sequences in such a radiation were distinct from other genes in the cluster but not from each other in the clade, making it difficult to assign trustworthy reference-based orthologies when multiple reference genes were present in the radiation. Consequently, NLR genes can be broadly divided into two types: radiating or high-fidelity, where high-fidelity genes are well conserved and well separated from other clades. A similar distinction could be made for NLR clusters, depending on whether cluster size was determined primarily by extensive radiation or the presence of numerous high-fidelity genes. We also identified groups of well-conserved NLR clades that were missing from the Columbia-0 reference genome. This suggests that the classification of NLRs using gene IDs from a single reference accession can rarely capture all major paralogs in a cluster accurately and representatively and that a reference-agnostic perspective is required to properly characterize these additional variations. Finally, we present a quantitative visualization method for differentiating these situations in a given clade of interest.
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Affiliation(s)
- Rachelle R.Q. Lee
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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35
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Pogoda M, Liu F, Douchkov D, Djamei A, Reif JC, Schweizer P, Schulthess AW. Identification of novel genetic factors underlying the host-pathogen interaction between barley (Hordeum vulgare L.) and powdery mildew (Blumeria graminis f. sp. hordei). PLoS One 2020; 15:e0235565. [PMID: 32614894 PMCID: PMC7332009 DOI: 10.1371/journal.pone.0235565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Powdery mildew is an important foliar disease of barley (Hordeum vulgare L.) caused by the biotrophic fungus Blumeria graminis f. sp. hordei (Bgh). The understanding of the resistance mechanism is essential for future resistance breeding. In particular, the identification of race-nonspecific resistance genes is important because of their regarded durability and broad-spectrum activity. We assessed the severity of powdery mildew infection on detached seedling leaves of 267 barley accessions using two poly-virulent isolates and performed a genome-wide association study exploiting 201 of these accessions. Two-hundred and fourteen markers, located on six barley chromosomes are associated with potential race-nonspecific Bgh resistance or susceptibility. Initial steps for the functional validation of four promising candidates were performed based on phenotype and transcription data. Specific candidate alleles were analyzed via transient gene silencing as well as transient overexpression. Microarray data of the four selected candidates indicate differential regulation of the transcription in response to Bgh infection. Based on our results, all four candidate genes seem to be involved in the responses to powdery mildew attack. In particular, the transient overexpression of specific alleles of two candidate genes, a potential arabinogalactan protein and the barley homolog of Arabidopsis thaliana’s Light-Response Bric-a-Brac/-Tramtrack/-Broad Complex/-POxvirus and Zinc finger (AtLRB1) or AtLRB2, were top candidates of novel powdery mildew susceptibility genes.
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Affiliation(s)
- Maria Pogoda
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Dimitar Douchkov
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Armin Djamei
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Patrick Schweizer
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Albert W. Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- * E-mail:
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36
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He H, Ji J, Li H, Tong J, Feng Y, Wang X, Han R, Bie T, Liu C, Zhu S. Genetic Diversity and Evolutionary Analyses Reveal the Powdery Mildew Resistance Gene Pm21 Undergoing Diversifying Selection. Front Genet 2020; 11:489. [PMID: 32477413 PMCID: PMC7241504 DOI: 10.3389/fgene.2020.00489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is a devastating disease that threatens wheat production and yield worldwide. The powdery mildew resistance gene Pm21, originating from wheat wild relative Dasypyrum villosum, encodes a coiled-coil, nucleotide-binding site, leucine-rich repeat (CC-NBS-LRR) protein and confers broad-spectrum resistance to wheat powdery mildew. In the present study, we isolated 73 Pm21 alleles from different powdery mildew-resistant D. villosum accessions, among which, 38 alleles were non-redundant. Sequence analysis identified seven minor insertion-deletion (InDel) polymorphisms and 400 single nucleotide polymorphisms (SNPs) among the 38 non-redundant Pm21 alleles. The nucleotide diversity of the LRR domain was significantly higher than those of the CC and NB-ARC domains. Further evolutionary analysis indicated that the solvent-exposed LRR residues of Pm21 alleles had undergone diversifying selection (dN/dS = 3.19734). In addition, eight LRR motifs and four amino acid sites in the LRR domain were also experienced positive selection, indicating that these motifs and sites play critical roles in resistance specificity. The phylogenetic tree showed that 38 Pm21 alleles were divided into seven classes. Classes A (including original Pm21), B and C were the major classes, including 26 alleles (68.4%). We also identified three non-functional Pm21 alleles from four susceptible homozygous D. villosum lines (DvSus-1 to DvSus-4) and two susceptible wheat-D. villosum chromosome addition lines (DA6V#1 and DA6V#3). The genetic variations of non-functional Pm21 alleles involved point mutation, deletion and insertion, respectively. The results also showed that the non-functional Pm21 alleles in the two chromosome addition lines both came from the susceptible donors of D. villosum. This study gives a new insight into the evolutionary characteristics of Pm21 alleles and discusses how to sustainably utilize Pm21 in wheat production. This study also reveals the sequence variants and origins of non-functional Pm21 alleles in D. villosum populations.
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Affiliation(s)
- Huagang He
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jian Ji
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hongjie Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Tong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yongqiang Feng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xiaolu Wang
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ran Han
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Tongde Bie
- Yangzhou Academy of Agricultural Sciences, Yangzhou, China
| | - Cheng Liu
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shanying Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.,School of Environment, Jiangsu University, Zhenjiang, China
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Klymiuk V, Fatiukha A, Raats D, Bocharova V, Huang L, Feng L, Jaiwar S, Pozniak C, Coaker G, Dubcovsky J, Fahima T. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2561-2572. [PMID: 31942623 PMCID: PMC7210774 DOI: 10.1093/jxb/eraa020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/12/2020] [Indexed: 05/21/2023]
Abstract
The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.
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Affiliation(s)
- Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Dina Raats
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lin Huang
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lihua Feng
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Correspondence:
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38
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Cai Y, Cai X, Wang Q, Wang P, Zhang Y, Cai C, Xu Y, Wang K, Zhou Z, Wang C, Geng S, Li B, Dong Q, Hou Y, Wang H, Ai P, Liu Z, Yi F, Sun M, An G, Cheng J, Zhang Y, Shi Q, Xie Y, Shi X, Chang Y, Huang F, Chen Y, Hong S, Mi L, Sun Q, Zhang L, Zhou B, Peng R, Zhang X, Liu F. Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:814-828. [PMID: 31479566 PMCID: PMC7004908 DOI: 10.1111/pbi.13249] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 05/09/2023]
Abstract
The diploid wild cotton species Gossypium australe possesses excellent traits including resistance to disease and delayed gland morphogenesis, and has been successfully used for distant breeding programmes to incorporate disease resistance traits into domesticated cotton. Here, we sequenced the G. australe genome by integrating PacBio, Illumina short read, BioNano (DLS) and Hi-C technologies, and acquired a high-quality reference genome with a contig N50 of 1.83 Mb and a scaffold N50 of 143.60 Mb. We found that 73.5% of the G. australe genome is composed of various repeat sequences, differing from those of G. arboreum (85.39%), G. hirsutum (69.86%) and G. barbadense (69.83%). The G. australe genome showed closer collinear relationships with the genome of G. arboreum than G. raimondii and has undergone less extensive genome reorganization than the G. arboreum genome. Selection signature and transcriptomics analyses implicated multiple genes in disease resistance responses, including GauCCD7 and GauCBP1, and experiments revealed induction of both genes by Verticillium dahliae and by the plant hormones strigolactone (GR24), salicylic acid (SA) and methyl jasmonate (MeJA). Experiments using a Verticillium-resistant domesticated G. barbadense cultivar confirmed that knockdown of the homologues of these genes caused a significant reduction in resistance against Verticillium dahliae. Moreover, knockdown of a newly identified gland-associated gene GauGRAS1 caused a glandless phenotype in partial tissues using G. australe. The G. australe genome represents a valuable resource for cotton research and distant relative breeding as well as for understanding the evolutionary history of crop genomes.
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Affiliation(s)
- Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Xiaoyan Cai
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Qinglian Wang
- School of Life Science and TechnologyHenan Institute of Science and TechnologyCollaborative Innovation Center of Modern Biological Breeding of Henan ProvinceHenan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and WheatXinxiangChina
| | - Ping Wang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Yu Zhang
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Yanchao Xu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Kunbo Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhongli Zhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Chenxiao Wang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Shuaipeng Geng
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Bo Li
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Qi Dong
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yuqing Hou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Heng Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Peng Ai
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Zhen Liu
- Anyang Institute of TechnologyAnyangChina
| | - Feifei Yi
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Minshan Sun
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Guoyong An
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Jieru Cheng
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Yuanyuan Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Qian Shi
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Yuanhui Xie
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Xinying Shi
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Ying Chang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Feifei Huang
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Yun Chen
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Shimiao Hong
- Guangzhou Genedenovo Biotechnology Co. LtdGuangzhouChina
| | - Lingyu Mi
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Quan Sun
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Lin Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | | | | | - Xiao Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesBioinformatics CenterSchool of Computer and Information EngineeringHenan UniversityKaifengChina
| | - Fang Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
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Leng Y, Zhao M, Fiedler J, Dreiseitl A, Chao S, Li X, Zhong S. Molecular Mapping of Loci Conferring Susceptibility to Spot Blotch and Resistance to Powdery Mildew in Barley Using the Sequencing-Based Genotyping Approach. PHYTOPATHOLOGY 2020; 110:440-446. [PMID: 31609681 DOI: 10.1094/phyto-08-19-0292-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spot blotch (SB) caused by Bipolaris sorokiniana and powdery mildew (PM) caused by Blumeria graminis f. sp. hordei are two important diseases of barley. To map genetic loci controlling susceptibility and resistance to these diseases, a mapping population consisting of 138 recombinant inbred lines (RILs) was developed from the cross between Bowman and ND5883. A genetic map was constructed for the population with 852 unique single nucleotide polymorphism markers generated by sequencing-based genotyping. Bowman and ND5883 showed distinct infection responses at the seedling stage to two isolates (ND90Pr and ND85F) of Bipolaris sorokiniana and one isolate (Race I) of Blumeria graminis f. sp. hordei. Genetic analysis of the RILs revealed that one major gene (Scs6) controls susceptibility to Bipolaris sorokiniana isolate ND90Pr, and another major gene (Mla8) confers resistance to Blumeria graminis f. sp. hordei isolate Race I, respectively. Scs6 was mapped on chromosome 1H of Bowman, as previously reported. Mla8 was also mapped to the short arm of 1H, which was tightly linked but not allelic to the Rcs6/Scs6 locus. Quantitative trait locus (QTL) analysis identified two QTLs, QSbs-1H-P1 and QSbs-7H-P1, responsible for susceptibility to spot blotch caused by Bipolaris sorokiniana isolate ND85F in ND5883, which are located on chromosome 1H and 7H, respectively. QSbs-7H-P1 was mapped to the same region as Rcs5, whereas QSbs-1H-P1 may represent a novel allele conferring seedling stage susceptibility to isolate ND85F. Identification and molecular mapping of the loci for SB susceptibility and PM resistance will facilitate development of barley cultivars with resistance to the diseases.
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Affiliation(s)
- Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Mingxia Zhao
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Jason Fiedler
- Department of Plant Science, North Dakota State University, Fargo, ND 58102, U.S.A
- U.S. Department of Agriculture-Agriculture Research Service Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | | | - Shiaoman Chao
- U.S. Department of Agriculture-Agriculture Research Service Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | - Xuehui Li
- Department of Plant Science, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
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40
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Frantzeskakis L, Di Pietro A, Rep M, Schirawski J, Wu CH, Panstruga R. Rapid evolution in plant-microbe interactions - a molecular genomics perspective. THE NEW PHYTOLOGIST 2020; 225:1134-1142. [PMID: 31134629 DOI: 10.1111/nph.15966] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Rapid (co-)evolution at multiple timescales is a hallmark of plant-microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights into genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathogens. These comprise fresh insights in allelic series of matching pairs of resistance and avirulence genes, the generation of novel pathogen effectors, the recently recognised small RNA warfare, and genomic aspects of secondary metabolite biosynthesis. In addition, we discuss the putative contributions of permissive host environments, transcriptional plasticity and the role of ploidy on the interactions. We conclude that the means underlying the rapid evolution of plant-microbe interactions are multifaceted and depend on the particular nature of each interaction.
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Affiliation(s)
| | - Antonio Di Pietro
- Departamento de Genética and Campus de Excelencia Agroalimentario (ceiA3), Universidad de Córdoba, 14071, Córdoba, Spain
| | - Martijn Rep
- Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94215, 1090 GE, Amsterdam, the Netherlands
| | - Jan Schirawski
- Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, Aachen, 52056, Germany
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41
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Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D, Keller B. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun 2019; 10:2292. [PMID: 31123263 PMCID: PMC6533294 DOI: 10.1038/s41467-019-10274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity.
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Affiliation(s)
- Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
| | - Lukas Kunz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Carol Kälin
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Michael Schläfli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Patrick Ackermann
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Science, ARO-Volcani Center, 50250, Bet Dagan, Israel
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Lindner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China.
- College of Life Science, Wuhan University, Wuhan, 430072, China.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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Sánchez-Martín J, Keller B. Contribution of recent technological advances to future resistance breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:713-732. [PMID: 30756126 DOI: 10.1007/s00122-019-03297-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/02/2019] [Indexed: 05/23/2023]
Abstract
The development of durable host resistance strategies to control crop diseases is a primary need for sustainable agricultural production in the future. This article highlights the potential of recent progress in the understanding of host resistance for future cereal breeding. Much of the novel work is based on advancements in large-scale sequencing and genomics, rapid gene isolation techniques and high-throughput molecular marker technologies. Moreover, emerging applications on the pathogen side like effector identification or field pathogenomics are discussed. The combination of knowledge from both sides of cereal pathosystems will result in new approaches for resistance breeding. We describe future applications and innovative strategies to implement effective and durable strategies to combat diseases of major cereal crops while reducing pesticide dependency.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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43
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Saur IML, Bauer S, Kracher B, Lu X, Franzeskakis L, Müller MC, Sabelleck B, Kümmel F, Panstruga R, Maekawa T, Schulze-Lefert P. Multiple pairs of allelic MLA immune receptor-powdery mildew AVR A effectors argue for a direct recognition mechanism. eLife 2019; 8:e44471. [PMID: 30777147 PMCID: PMC6414202 DOI: 10.7554/elife.44471] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 01/03/2023] Open
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins in plants and animals mediate intracellular pathogen sensing. Plant NLRs typically detect strain-specific pathogen effectors and trigger immune responses often linked to localized host cell death. The barley Mla disease resistance locus has undergone extensive functional diversification in the host population and encodes numerous allelic NLRs each detecting a matching isolate-specific avirulence effector (AVRA) of the fungal pathogen Blumeria graminis f. sp. hordei (Bgh). We report here the isolation of Bgh AVRa7, AVRa9, AVRa10, and AVRa22, which encode small secreted proteins recognized by allelic MLA7, MLA9, MLA10, and MLA22 receptors, respectively. These effectors are sequence-unrelated, except for allelic AVRa10 and AVRa22 that are co-maintained in pathogen populations in the form of a balanced polymorphism. Contrary to numerous examples of indirect recognition of bacterial effectors by plant NLRs, co-expression experiments with matching Mla-AVRa pairs indicate direct detection of the sequence-unrelated fungal effectors by MLA receptors.
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Affiliation(s)
- Isabel ML Saur
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Saskia Bauer
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Barbara Kracher
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Xunli Lu
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lamprinos Franzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Marion C Müller
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Takaki Maekawa
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Paul Schulze-Lefert
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant SciencesDüsseldorfGermany
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44
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Ma Y, Liu M, Stiller J, Liu C. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics 2019; 20:12. [PMID: 30616511 PMCID: PMC6323845 DOI: 10.1186/s12864-018-5357-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/09/2018] [Indexed: 11/12/2022] Open
Abstract
Background It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. Electronic supplementary material The online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanling Ma
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Miao Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.,Crop Research Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jiri Stiller
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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45
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Maekawa T, Kracher B, Saur IML, Yoshikawa-Maekawa M, Kellner R, Pankin A, von Korff M, Schulze-Lefert P. Subfamily-Specific Specialization of RGH1/MLA Immune Receptors in Wild Barley. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:107-119. [PMID: 30295580 DOI: 10.1094/mpmi-07-18-0186-fi] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The barley disease resistance (R) gene locus mildew locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis hordei and has been introgressed into modern cultivars from diverse germplasms, including the wild relative Hordeum spontaneum. Known Mla disease resistance specificities to B. graminis hordei appear to encode allelic variants of the R gene homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Here, we sequenced and assembled the transcriptomes of 50 H. spontaneum accessions representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, linked neither to geographic origin nor population structure, and could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil (CC) signaling domains that are both capable of eliciting cell death. The presence of positively selected sites located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both CC signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the population. Unexpectedly, known MLA receptor variants that confer B. graminis hordei resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially as adaptation to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor. Copyright © 2018 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)
- Takaki Maekawa
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Barbara Kracher
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Isabel M L Saur
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | | | - Ronny Kellner
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Artem Pankin
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Maria von Korff
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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46
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Bourras S, Praz CR, Spanu PD, Keller B. Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen. Curr Opin Microbiol 2018; 46:26-33. [DOI: 10.1016/j.mib.2018.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/25/2023]
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47
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Habachi-Houimli Y, Khalfallah Y, Mezghani-Khemakhem M, Makni H, Makni M, Bouktila D. Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley. 3 Biotech 2018; 8:453. [PMID: 30370194 DOI: 10.1007/s13205-018-1478-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/11/2018] [Indexed: 12/29/2022] Open
Abstract
In this study, a systematic analysis of Nucleotide-Binding Site (NBS) disease resistance (R) gene family in the barley, Hordeum vulgare L. cv. Bowman, genome was performed. Using multiple computational analyses, we could identify 96 regular NBS-encoding genes and characterize them on the bases of structural diversity, conserved protein signatures, genomic distribution, gene duplications, differential expression, selection pressure, codon usage, regulation by microRNAs and phylogenetic relationships. Depending on the presence or absence of CC and LRR domains; the identified NBS genes were assigned to four distinct groups; NBS-LRR (53.1%), CC-NBS-LRR (14.6%), NBS (26%), and CC-NBS (6.3%). NBS-associated domain analysis revealed the presence of signal peptides, zinc fingers, diverse kinases, and other structural features. Eighty-five of the identified NBS-encoding genes were mapped onto the seven barley chromosomes, revealing that 50% of them were located on chromosomes 7H, 2H, and 3H, with a tendency of NBS genes to be clustered in the distal telomeric regions of the barley chromosomes. Nine gene clusters, representing 22.35% of total mapped barley NBS-encoding genes, were found, suggesting that tandem duplication stands for an important mechanism in the expansion of this gene family in barley. Phylogenetic analysis determined 31 HvNBS orthologs from rice and Brachypodium. 87 out of 96 HvNBSs were supported by expression evidence, exhibiting various and quantitatively uneven expression patterns across distinct tissues, organs, and development stages. Fourteen potential miRNA-R gene target pairs were further identified, providing insight into the regulation of NBS genes expression. These findings offer candidate target genes to engineer disease-resistant barley genotypes, and promote our understanding of the evolution of NBS-encoding genes in Poaceae crops.
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Affiliation(s)
- Yosra Habachi-Houimli
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Yosra Khalfallah
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani-Khemakhem
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Hanem Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 2Université de Tunis, Institut Supérieur de l'Animation pour la Jeunesse et la Culture (ISAJC), Bir El Bey, Tunisia
| | - Mohamed Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Dhia Bouktila
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 3Université de Jendouba, Institut Supérieur de Biotechnologie de Béja (ISBB), 9000 Béja, Tunisia
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Davis JL, Armengaud P, Larson TR, Graham IA, White PJ, Newton AC, Amtmann A. Contrasting nutrient-disease relationships: Potassium gradients in barley leaves have opposite effects on two fungal pathogens with different sensitivities to jasmonic acid. PLANT, CELL & ENVIRONMENT 2018; 41:2357-2372. [PMID: 29851096 PMCID: PMC6175101 DOI: 10.1111/pce.13350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/21/2018] [Indexed: 05/20/2023]
Abstract
Understanding the interactions between mineral nutrition and disease is essential for crop management. Our previous studies with Arabidopsis thaliana demonstrated that potassium (K) deprivation induced the biosynthesis of jasmonic acid (JA) and increased the plant's resistance to herbivorous insects. Here, we addressed the question of how tissue K affects the development of fungal pathogens and whether sensitivity of the pathogens to JA could play a role for the K-disease relationship in barley (Hordeum vulgare cv. Optic). We report that K-deprived barley plants showed increased leaf concentrations of JA and other oxylipins. Furthermore, a natural tip-to-base K-concentration gradient within leaves of K-sufficient plants was quantitatively mirrored by the transcript levels of JA-responsive genes. The local leaf tissue K concentrations affected the development of two economically important fungi in opposite ways, showing a positive correlation with powdery mildew (Blumeria graminis) and a negative correlation with leaf scald (Rhynchosporium commune) disease symptoms. B. graminis induced a JA response in the plant and was sensitive to methyl-JA treatment whereas R. commune initiated no JA response and was JA insensitive. Our study challenges the view that high K generally improves plant health and suggests that JA sensitivity of pathogens could be an important factor in determining the exact K-disease relationship.
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Affiliation(s)
- Jayne L. Davis
- Plant Science Group, Institute for Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
- Ecological SciencesThe James Hutton InstituteDundeeUK
| | - Patrick Armengaud
- Plant Science Group, Institute for Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Tony R. Larson
- Department of Biology, Centre for Novel Agricultural ProductsUniversity of YorkYorkUK
| | - Ian A. Graham
- Department of Biology, Centre for Novel Agricultural ProductsUniversity of YorkYorkUK
| | | | | | - Anna Amtmann
- Plant Science Group, Institute for Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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Singh SP, Hurni S, Ruinelli M, Brunner S, Sanchez-Martin J, Krukowski P, Peditto D, Buchmann G, Zbinden H, Keller B. Evolutionary divergence of the rye Pm17 and Pm8 resistance genes reveals ancient diversity. PLANT MOLECULAR BIOLOGY 2018; 98:249-260. [PMID: 30244408 DOI: 10.1007/s11103-018-0780-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/12/2018] [Indexed: 05/18/2023]
Abstract
We have isolated a novel powdery mildew resistance gene in wheat that was originally introgressed from rye. Further analysis revealed evolutionary divergent history of wheat and rye orthologous resistance genes. Wheat production is under constant threat from a number of fungal pathogens, among them is wheat powdery mildew (Blumeria graminis f. sp. tritici). Deployment of resistance genes is the most economical and sustainable method for mildew control. However, domestication and selective breeding have narrowed genetic diversity of modern wheat germplasm, and breeders have relied on wheat relatives for enriching its gene pool through introgression. Translocations where the 1RS chromosome arm was introgressed from rye to wheat have improved yield and resistance against various pathogens. Here, we isolated the Pm17 mildew resistance gene located on the 1RS introgression in wheat cultivar 'Amigo' and found that it is an allele or a close paralog of the Pm8 gene isolated earlier from 'Petkus' rye. Functional validation using transient and stable transformation confirmed the identity of Pm17. Analysis of Pm17 and Pm8 coding regions revealed an overall identity of 82.9% at the protein level, with the LRR domains being most divergent. Our analysis also showed that the two rye genes are much more diverse compared to the variants encoded by the Pm3 gene in wheat, which is orthologous to Pm17/Pm8 as concluded from highly conserved upstream sequences in all these genes. Thus, the evolutionary history of these orthologous loci differs in the cereal species rye and wheat and demonstrates that orthologous resistance genes can take different routes towards functionally active genes. These findings suggest that the isolation of Pm3/Pm8/Pm17 orthologs from other grass species, additional alleles from the rye germplasm as well as possibly synthetic variants will result in novel resistance genes useful in wheat breeding.
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Affiliation(s)
- Simrat Pal Singh
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- ETH Zürich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Michela Ruinelli
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Susanne Brunner
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Javier Sanchez-Martin
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Patricia Krukowski
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - David Peditto
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
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50
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Wu Y, Ma X, Pan Z, Kale SD, Song Y, King H, Zhang Q, Presley C, Deng X, Wei CI, Xiao S. Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew. BMC Genomics 2018; 19:705. [PMID: 30253736 PMCID: PMC6156980 DOI: 10.1186/s12864-018-5069-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici. RESULTS We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification. CONCLUSIONS Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.
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Affiliation(s)
- Ying Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xianfeng Ma
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, 410128 China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiv D. Kale
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Yi Song
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Harlan King
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Qiong Zhang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Christian Presley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cheng-I Wei
- College of Agriculture & Natural Resources, University of Maryland, College Park, MD 20742 USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
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