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Yang L. One stone, two birds: The barley NLR protein MLA3 recognizes the rice blast fungus effector Pwl2 in addition to its cognate effector AVRa3 from barley powdery mildew. THE PLANT CELL 2024; 36:223-224. [PMID: 37930323 PMCID: PMC10827308 DOI: 10.1093/plcell/koad275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Leiyun Yang
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Department of Plant Pathology, College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
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2
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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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3
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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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4
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Muria-Gonzalez MJ, Lawrence JA, Palmiero E, D'Souza NK, Gupta S, Ellwood SR. Major Susceptibility Gene Epistasis over Minor Gene Resistance to Spot Form Net Blotch in a Commercial Barley Cultivar. PHYTOPATHOLOGY 2023; 113:1058-1065. [PMID: 37454241 DOI: 10.1094/phyto-10-22-0376-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant global disease of barley (Hordeum vulgare). Baudin, a barley cultivar that was until recently extensively grown in Western Australia, was reported as having minor seedling resistance. However, Baudin was highly susceptible to a local isolate, M3, suggesting that this isolate had gained virulence against a major susceptibility gene. M3 causes atypical lesions with pale centers early in the infection, with initial screens of a segregating population indicating that this was determined by a single locus in the Baudin genome. The susceptibility was semidominant in F1 progeny and the susceptibility gene, designated Spm1 (Susceptibility to P. teres f. maculata 1), mapped to a 190-kb section of the resistance gene-rich Mla region of chromosome 1H. Phenotyping with Ptm SP1, a non-M3 pathotype, identified a seedling resistance locus on 2H. Minor gene resistance is generally regarded as potentially durable, but our findings suggest the resistance to spot form net blotch in Baudin is nullified by strong susceptibility conferred by a separate locus on 1H. [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)
- Mariano Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Julie A Lawrence
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Elzette Palmiero
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Nola K D'Souza
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Sanjiv Gupta
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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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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6
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Gou M, Balint-Kurti P, Xu M, Yang Q. Quantitative disease resistance: Multifaceted players in plant defense. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:594-610. [PMID: 36448658 DOI: 10.1111/jipb.13419] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
In contrast to large-effect qualitative disease resistance, quantitative disease resistance (QDR) exhibits partial and generally durable resistance and has been extensively utilized in crop breeding. The molecular mechanisms underlying QDR remain largely unknown but considerable progress has been made in this area in recent years. In this review, we summarize the genes that have been associated with plant QDR and their biological functions. Many QDR genes belong to the canonical resistance gene categories with predicted functions in pathogen perception, signal transduction, phytohormone homeostasis, metabolite transport and biosynthesis, and epigenetic regulation. However, other "atypical" QDR genes are predicted to be involved in processes that are not commonly associated with disease resistance, such as vesicle trafficking, molecular chaperones, and others. This diversity of function for QDR genes contrasts with qualitative resistance, which is often based on the actions of nucleotide-binding leucine-rich repeat (NLR) resistance proteins. An understanding of the diversity of QDR mechanisms and of which mechanisms are effective against which classes of pathogens will enable the more effective deployment of QDR to produce more durably resistant, resilient crops.
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Affiliation(s)
- Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Shennong Laboratory, Zhengzhou, 450002, China
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, USDA-ARS, Raleigh, NC, 27695, USA
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy, China Agricultural University, Beijing, 100193, China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, China
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7
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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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8
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Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat Genet 2022; 54:227-231. [PMID: 35288708 PMCID: PMC8920886 DOI: 10.1038/s41588-022-01022-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/25/2022] [Indexed: 12/19/2022]
Abstract
The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future. Chromosome-scale genome assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega facilitates the cloning of the stripe rust resistance gene Yr27.
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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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Pirrello C, Malacarne G, Moretto M, Lenzi L, Perazzolli M, Zeilmaker T, Van den Ackerveken G, Pilati S, Moser C, Giacomelli L. Grapevine DMR6-1 Is a Candidate Gene for Susceptibility to Downy mildew. Biomolecules 2022; 12:biom12020182. [PMID: 35204683 PMCID: PMC8961545 DOI: 10.3390/biom12020182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Grapevine (Vitis vinifera) is a valuable crop in Europe for both economical and cultural reasons, but highly susceptible to Downy mildew (DM). The generation of resistant vines is of critical importance for a sustainable viticulture and can be achieved either by introgression of resistance genes in susceptible varieties or by mutation of Susceptibility (S) genes, e.g., by gene editing. This second approach offers several advantages: it maintains the genetic identity of cultivars otherwise disrupted by crossing and generally results in a broad-spectrum and durable resistance, but it is hindered by the poor knowledge about S genes in grapevines. Candidate S genes are Downy mildew Resistance 6 (DMR6) and DMR6-Like Oxygenases (DLOs), whose mutations confer resistance to DM in Arabidopsis. In this work, we show that grapevine VviDMR6-1 complements the Arabidopsis dmr6-1 resistant mutant. We studied the expression of grapevine VviDMR6 and VviDLO genes in different organs and in response to the DM causative agent Plasmopara viticola. Through an automated evaluation of causal relationships among genes, we show that VviDMR6-1, VviDMR6-2, and VviDLO1 group into different co-regulatory networks, suggesting distinct functions, and that mostly VviDMR6-1 is connected with pathogenesis-responsive genes. Therefore, VviDMR6-1 represents a good candidate to produce resistant cultivars with a gene-editing approach.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Giulia Malacarne
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
| | - Luisa Lenzi
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
- Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Stefania Pilati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy; (C.P.); (G.M.); (M.M.); (L.L.); (M.P.); (S.P.); (C.M.)
- Correspondence:
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11
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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: 20] [Impact Index Per Article: 6.7] [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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12
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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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13
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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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14
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Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Šimková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. THE PLANT CELL 2021; 33:1888-1906. [PMID: 33710295 PMCID: PMC8290290 DOI: 10.1093/plcell/koab077] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/28/2021] [Indexed: 05/19/2023]
Abstract
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | | | - Thomas Lux
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Jennifer Ens
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Heidrun Gundlach
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Lori B Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Samuel Holden
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | | | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
| | - Klaus F X Mayer
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Manuel Spannagl
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Curtis J Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen 37073, Germany
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15
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Qi LL, Talukder ZI, Ma GJ, Li XH. Discovery and mapping of two new rust resistance genes, R 17 and R 18, in sunflower using genotyping by sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2291-2301. [PMID: 33837443 DOI: 10.1007/s00122-021-03826-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Discovery of two rust resistance genes, R17 and R18, from the sunflower lines introduced from South Africa and genetic mapping of them to sunflower chromosome 13. Rust, caused by the fungus Puccinia helianthi Schw., is one of the most serious diseases of sunflower in the world. The rapid changes that occur in the virulence characteristics of pathogen populations present a continuous threat to the effectiveness of existing rust-resistant hybrids. Thus, there is a continued need for the characterization of genetically diverse sources of rust resistance. In this study, we report to identify two new rust resistance genes, R17 and R18, from the sunflower lines, KP193 and KP199, introduced from South Africa. The inheritance of rust resistance was investigated in both lines using two mapping populations developed by crossing the resistant plants selected from KP193 and KP199 with a common susceptible parent HA 89. The F2 populations were first genotyped using genotyping by sequencing for mapping of the rust genes and further saturated with markers in the target region. Molecular mapping positioned the two genes at the lower end of sunflower chromosome 13 within a large gene cluster. Two co-segregating SNP markers, SFW01497 and SFW08875, were distal to R17 at a 1.9 cM genetic distance, and a cluster of five co-segregating SNPs was proximal to R17 at 0.7 cM. R18 co-segregated with the SNP marker SFW04317 and was proximal to two cosegregating SNPs, SFW01497 and SFW05453, at 1.9 cM. These maps provide markers for stacking R17 or R18 with other broadly effective rust resistance genes to extend the durability of rust resistance. The relationship of the six rust resistance genes in the cluster was discussed.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - X H Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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16
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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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17
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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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18
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Bhattarai K, Conesa A, Xiao S, Peres NA, Clark DG, Parajuli S, Deng Z. Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance. BMC PLANT BIOLOGY 2020; 20:539. [PMID: 33256589 PMCID: PMC7706040 DOI: 10.1186/s12870-020-02742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/16/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy is one of the most important flowers in the global floricultural trade, and powdery mildew (PM) is the most important disease of gerbera. Genetic improvement of gerbera PM resistance has become a crucial goal in gerbera breeding. A better understanding of the genetic control of gerbera resistance to PM can expedite the development of PM-resistant cultivars. RESULTS The objectives of this study were to identify gerbera genotypes with contrasting phenotypes in PM resistance and sequence and analyze their leaf transcriptomes to identify disease resistance and susceptibility genes differentially expressed and associated with PM resistance. An additional objective was to identify SNPs and SSRs for use in future genetic studies. We identified two gerbera genotypes, UFGE 4033 and 06-245-03, that were resistant and susceptible to PM, respectively. De novo assembly of their leaf transcriptomes using four complementary pipelines resulted in 145,348 transcripts with a N50 of 1124 bp, of which 67,312 transcripts contained open reading frames and 48,268 were expressed in both genotypes. A total of 494 transcripts were likely involved in disease resistance, and 17 and 24 transcripts were up- and down-regulated, respectively, in UFGE 4033 compared to 06-245-03. These gerbera disease resistance transcripts were most similar to the NBS-LRR class of plant resistance genes conferring resistance to various pathogens in plants. Four disease susceptibility transcripts (MLO-like) were expressed only or highly expressed in 06-245-03, offering excellent candidate targets for gene editing for PM resistance in gerbera. A total of 449,897 SNPs and 19,393 SSRs were revealed in the gerbera transcriptomes, which can be a valuable resource for developing new molecular markers. CONCLUSION This study represents the first transcriptomic analysis of gerbera PM resistance, a highly important yet complex trait in a globally important floral crop. The differentially expressed disease resistance and susceptibility transcripts identified provide excellent targets for development of molecular markers and genetic maps, cloning of disease resistance genes, or targeted mutagenesis of disease susceptibility genes for PM resistance in gerbera.
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Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, IFAS, Gainesville, FL, 32611, USA
- University of Florida, Genetics Institute, Gainesville, FL, 32611, USA
| | - Shunyuan Xiao
- University of Maryland, College of Agriculture and Natural Resources, 4291 Fieldhouse Drive, Rockville, MD, 20850, USA
| | - Natalia A Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, 32611, USA
| | - Saroj Parajuli
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA.
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19
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Md Hatta MA, Ghosh S, Athiyannan N, Richardson T, Steuernagel B, Yu G, Rouse MN, Ayliffe M, Lagudah ES, Radhakrishnan GV, Periyannan SK, Wulff BBH. Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1286-1298. [PMID: 32779520 DOI: 10.1094/mpmi-01-20-0018-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici, has reemerged as a major threat to wheat cultivation. The stem rust (Sr) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare, which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum, which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 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)
- M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Naveenkumar Athiyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Matthew N Rouse
- United States Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Sambasivam K Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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20
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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21
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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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22
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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: 53] [Impact Index Per Article: 13.3] [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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23
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Oganesyants L, Vafin R, Galstyan A, Ryabova A, Khurshudyan S, Semipyatniy V. DNA authentication of brewery products: basic principles and methodological approaches. FOODS AND RAW MATERIALS 2019. [DOI: 10.21603/2308-4057-2019-2-364-374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Beer DNA authentication is the process of authentication by identification of barley malt Hordeum vulgare or its substitutes, as well as hops and yeast. The method is based on molecular genetic analysis of residual quantities of nucleic acids extracted from the cellular debris of the final product. The aim of the study was to analyse scientific and methodical approaches to extraction of residual quantities of beer raw materials nucleic acids and beer DNA authentication for their later application in determining brewing products authenticity. The technological level discloses the method of DNA extraction from wines, modified for extraction of nucleic acids from beer samples. The method includes the following characteristic peculiarities: stage enzymatic hydrolysis of polysaccharides and polypeptides of dissolved lyophilisate, multiple sedimentation and resursuspension of nucleoproteid complex, RNA removal followed by DNA extraction by organic solvents, and additional DNA purification by magnetic particle adsorption. This review presents the analysis of genetic targets used as molecular markers for gene identification of malting barley varieties and beer DNA authentication. We also provided the interpretation of PCR analysis of Hordeum vulgare varieties and samples of commercial beer. Data on SSR- and SNP-markers of Hordeum vulgare nuclear DNA, used for barley varieties identification and potentially suitable for beer DNA authentication, are also presented. We also analysed genetic targets used in malting barley substitute detection, as well as hops and yeast identification in beer. Data on correlation of amplified DNA targets with beer quality indicators were systematised.
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Affiliation(s)
- Lev Oganesyants
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Ramil Vafin
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Aram Galstyan
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Anastasia Ryabova
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Sergey Khurshudyan
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Vladislav Semipyatniy
- All-Russian Scientific Research Institute of Brewing, Non-Alcoholic and Wine Industry
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24
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Lahari Z, Ribeiro A, Talukdar P, Martin B, Heidari Z, Gheysen G, Price AH, Shrestha R. QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice ( Oryza sativa L.). EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2019; 215:117. [PMID: 31274875 PMCID: PMC6570777 DOI: 10.1007/s10681-019-2427-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/27/2019] [Indexed: 05/31/2023]
Abstract
The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite's life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F2 progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20 and 23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification.
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Affiliation(s)
- Zobaida Lahari
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Antonio Ribeiro
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Partha Talukdar
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Brennan Martin
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Zeynab Heidari
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Godelieve Gheysen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Adam H. Price
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Roshi Shrestha
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
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25
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Dracatos PM, Bartoš J, Elmansour H, Singh D, Karafiátová M, Zhang P, Steuernagel B, Svačina R, Cobbin JCA, Clark B, Hoxha S, Khatkar MS, Doležel J, Wulff BB, Park RF. The Coiled-Coil NLR Rph1, Confers Leaf Rust Resistance in Barley Cultivar Sudan. PLANT PHYSIOLOGY 2019; 179:1362-1372. [PMID: 30593453 PMCID: PMC6446784 DOI: 10.1104/pp.18.01052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/18/2018] [Indexed: 05/18/2023]
Abstract
Unraveling and exploiting mechanisms of disease resistance in cereal crops is currently limited by their large repeat-rich genomes and the lack of genetic recombination or cultivar (cv)-specific sequence information. We cloned the first leaf rust resistance gene Rph1 (Rph1 a) from cultivated barley (Hordeum vulgare) using "MutChromSeq," a recently developed molecular genomics tool for the rapid cloning of genes in plants. Marker-trait association in the CI 9214/Stirling doubled haploid population mapped Rph1 to the short arm of chromosome 2H in a physical region of 1.3 megabases relative to the barley cv Morex reference assembly. A sodium azide mutant population in cv Sudan was generated and 10 mutants were confirmed by progeny-testing. Flow-sorted 2H chromosomes from Sudan (wild type) and six of the mutants were sequenced and compared to identify candidate genes for the Rph1 locus. MutChromSeq identified a single gene candidate encoding a coiled-coil nucleotide binding site Leucine-rich repeat (NLR) receptor protein that was altered in three different mutants. Further Sanger sequencing confirmed all three mutations and identified an additional two independent mutations within the same candidate gene. Phylogenetic analysis determined that Rph1 clustered separately from all previously cloned NLRs from the Triticeae and displayed highest sequence similarity (89%) with a homolog of the Arabidopsis (Arabidopsis thaliana) disease resistance protein 1 protein in Triticum urartu In this study we determined the molecular basis for Rph1-mediated resistance in cultivated barley enabling varietal improvement through diagnostic marker design, gene editing, and gene stacking technologies.
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Affiliation(s)
- Peter Michael Dracatos
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Huda Elmansour
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Davinder Singh
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Peng Zhang
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | | | - Radim Svačina
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Joanna C A Cobbin
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bethany Clark
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Sami Hoxha
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Mehar S Khatkar
- Faculty of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | | | - Robert F Park
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
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26
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Bayer PE, Golicz AA, Tirnaz S, Chan CK, Edwards D, Batley J. Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:789-800. [PMID: 30230187 PMCID: PMC6419861 DOI: 10.1111/pbi.13015] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/16/2018] [Accepted: 09/14/2018] [Indexed: 05/19/2023]
Abstract
Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVic.Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Chon‐Kit Kenneth Chan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- Australian Genome Research FacilityMelbourneVic.Australia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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27
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Monat C, Schreiber M, Stein N, Mascher M. Prospects of pan-genomics in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:785-796. [PMID: 30446793 DOI: 10.1007/s00122-018-3234-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/07/2018] [Indexed: 05/10/2023]
Abstract
The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural diversity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large diversity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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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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29
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Rajaraman J, Douchkov D, Lück S, Hensel G, Nowara D, Pogoda M, Rutten T, Meitzel T, Brassac J, Höfle C, Hückelhoven R, Klinkenberg J, Trujillo M, Bauer E, Schmutzer T, Himmelbach A, Mascher M, Lazzari B, Stein N, Kumlehn J, Schweizer P. Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance. Genome Biol 2018; 19:116. [PMID: 30111359 PMCID: PMC6092874 DOI: 10.1186/s13059-018-1472-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/04/2018] [Indexed: 11/11/2022] Open
Abstract
Background The large and highly repetitive genomes of the cultivated species Hordeum vulgare (barley), Triticum aestivum (wheat), and Secale cereale (rye) belonging to the Triticeae tribe of grasses appear to be particularly rich in gene-like sequences including partial duplicates. Most of them have been classified as putative pseudogenes. In this study we employ transient and stable gene silencing- and over-expression systems in barley to study the function of HvARM1 (for H. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15 (for H. vulgare Plant U-Box 15). Results The partial ARM1 gene is derived from a gene-duplication event in a common ancestor of the Triticeae and contributes to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungus Blumeria graminis. In barley, allelic variants of HvARM1 but not of HvPUB15 are significantly associated with levels of powdery mildew infection. Both HvPUB15 and HvARM1 proteins interact in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) of Arabidopsis thaliana. A genome-wide scan for partial gene duplicates reveals further events in barley resulting in stress-regulated, potentially neo-functionalized, genes. Conclusion The results suggest neo-functionalization of the partial gene copy HvARM1 increases resistance against powdery mildew infection. It further links plastid function with susceptibility to biotrophic pathogen attack. These findings shed new light on a novel mechanism to employ partial duplication of protein-protein interaction domains to facilitate the expansion of immune signaling networks. Electronic supplementary material The online version of this article (10.1186/s13059-018-1472-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeyaraman Rajaraman
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Dimitar Douchkov
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Stefanie Lück
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Daniela Nowara
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Maria Pogoda
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Twan Rutten
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Tobias Meitzel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jonathan Brassac
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Caroline Höfle
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ralph Hückelhoven
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Jörn Klinkenberg
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Marco Trujillo
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany.,Albert-Ludwigs-Universität Freiburg, Institut für Biologie II, Zellbiologie, D-79104, Freiburg, Germany
| | - Eva Bauer
- Technische Universität München, Liesel-Beckmann-Straße 2, D-85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Barbara Lazzari
- Parco Technologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy
| | - Nils Stein
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Patrick Schweizer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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30
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Upson JL, Zess EK, Białas A, Wu CH, Kamoun S. The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:108-116. [PMID: 29604609 DOI: 10.1016/j.pbi.2018.03.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 05/11/2023]
Abstract
Plant-microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales. However, mechanistic research on plant-microbe interactions has often been conducted with little consideration of evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the range of mechanisms and models from the molecular plant-microbe interactions field. In recent years, the incipient field of evolutionary molecular plant-microbe interactions (EvoMPMI) has emerged to bridge this gap. Here, we report on some of the recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to expand our understanding of plant-microbe interactions.
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Affiliation(s)
- Jessica L Upson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Erin K Zess
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.
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31
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Leng Y, Zhao M, Wang R, Steffenson BJ, Brueggeman RS, Zhong S. The gene conferring susceptibility to spot blotch caused by Cochliobolus sativus is located at the Mla locus in barley cultivar Bowman. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1531-1539. [PMID: 29663053 DOI: 10.1007/s00122-018-3095-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
We identified, fine mapped, and physically anchored a dominant spot blotch susceptibility gene Scs6 to a 125 kb genomic region containing the Mla locus on barley chromosome 1H. Spot blotch caused by Cochliobolus sativus is an important disease of barley, but the molecular mechanisms underlying resistance and susceptibility to the disease are not well understood. In this study, we identified and mapped a gene conferring susceptibility to spot blotch caused by the pathotype 2 isolate (ND90Pr) of C. sativus in barley cultivar Bowman. Genetic analysis of F1 and F2 progeny as well as F3 families from a cross between Bowman and ND 5883 indicated that a single dominant gene (designated as Scs6) conferred spot blotch susceptibility in Bowman. Using a doubled haploid (DH) population derived from a cross between Calicuchima-sib (resistant) and Bowman-BC (susceptible), we confirmed that Scs6, contributed by Bowman-BC, was localized at the same locus as the previously identified spot blotch resistance allele Rcs6, which was contributed by Calicuchima-sib and mapped on the short arm of chromosome 1H. Using a genome-wide putative linear gene index of barley (Genome Zipper), 13 cleaved amplified polymorphism markers were developed from 11 flcDNA and two EST sequences and mapped to the Scs6/Rcs6 region on a linkage map constructed with the DH population. Further fine mapping with markers developed from barley genome sequences and F2 recombinants derived from Bowman × ND 5883 and Bowman × ND B112 crosses delimited Scs6 in a 125 kb genomic interval harboring the Mla locus on the reference genome of barley cv. Morex. This study provides a foundational step for further cloning of Scs6 using a map-based approach.
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Affiliation(s)
- Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Mingxia Zhao
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Rui Wang
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.
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32
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Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. MOLECULAR PLANT PATHOLOGY 2018; 19:1267-1281. [PMID: 28834153 PMCID: PMC6638128 DOI: 10.1111/mpp.12607] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
- College of Life SciencesFujian Agricultural and Forestry UniversityFuzhouFujian 350002China
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
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33
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Losvik A, Beste L, Stephens J, Jonsson L. Overexpression of the aphid-induced serine protease inhibitor CI2c gene in barley affects the generalist green peach aphid, not the specialist bird cherry-oat aphid. PLoS One 2018; 13:e0193816. [PMID: 29554141 PMCID: PMC5858787 DOI: 10.1371/journal.pone.0193816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
Aphids are serious pests in crop plants. In an effort to identify plant genes controlling resistance against aphids, we have here studied a protease inhibitor, CI2c in barley (Hordeum vulgare L.). The CI2c gene was earlier shown to be upregulated by herbivory of the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley genotypes with moderate resistance against this aphid, but not in susceptible lines. We hypothesized that CI2c contributes to the resistance. To test this idea, cDNA encoding CI2c was overexpressed in barley and bioassays were carried out with R. padi. For comparison, tests were carried out with the green peach aphid (Myzus persicae Sulzer), for which barley is a poor host. The performance of R. padi was not different on the CI2c-overexpressing lines in comparison to controls in test monitoring behavior and fecundity. M. persicae preference was affected as shown in the choice test, this species moved away from control plants, but remained on the CI2c-overexpressing lines. R. padi-induced responses related to defense were repressed in the overexpressing lines as compared to in control plants or the moderately resistant genotypes. A putative susceptibility gene, coding for a β-1,3-glucanase was more strongly induced by aphids in one of the CI2c-overexpressing lines. The results indicate that the CI2c inhibitor in overexpressing lines affects aphid-induced responses by suppressing defense. This is of little consequence to the specialist R.padi, but causes lower non-host resistance towards the generalist M. persicae in barley.
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Affiliation(s)
- Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Lisa Beste
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Jennifer Stephens
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Lisbeth Jonsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail:
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Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. G3-GENES GENOMES GENETICS 2017; 7:3317-3329. [PMID: 28790145 PMCID: PMC5633382 DOI: 10.1534/g3.117.300125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Powdery mildew pathogens colonize over 9500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh. Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes (Chr) 2HL and 1HS. Within these regions reside diverse resistance loci derived from barley landrace H. laevigatum (MlLa) and H. vulgare cv. Algerian (Mla1), which associate with the altered expression of 961 and 3296 genes during fungal penetration of the host and haustorial development, respectively. Regulatory control of transcript levels for 299 of the 961 genes is reprioritized from MlLa on 2HL to Mla1 on 1HS as infection progresses, with 292 of the 299 alternating the allele responsible for higher expression, including Adaptin Protein-2 subunit μ AP2M and Vesicle Associated Membrane Protein VAMP72 subfamily members VAMP721/722. AP2M mediates effector-triggered immunity (ETI) via endocytosis of plasma membrane receptor components. VAMP721/722 and SNAP33 form a Soluble N-ethylmaleimide-sensitive factor Attachment Protein REceptor (SNARE) complex with SYP121 (PEN1), which is engaged in pathogen associated molecular pattern (PAMP)-triggered immunity via exocytosis. We postulate that genes regulated by alternate chromosomal positions are repurposed as part of a conserved immune complex to respond to different pathogen attack scenarios.
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35
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Baggs E, Dagdas G, Krasileva KV. NLR diversity, helpers and integrated domains: making sense of the NLR IDentity. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:59-67. [PMID: 28494248 DOI: 10.1016/j.pbi.2017.04.012] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 05/21/2023]
Abstract
Plant innate immunity relies on genetically predetermined repertoires of immune receptors to detect pathogens and trigger an effective immune response. A large proportion of these receptors are from the Nucletoide Binding Leucine Rich Repeat (NLR) gene family. As plants live longer than most pathogens, maintaining diversity of NLRs and deploying efficient 'pathogen traps' is necessary to withstand the evolutionary battle. In this review, we summarize the sources of diversity in NLR plant immune receptors giving an overview of genomic, regulatory as well as functional studies, including the latest concepts of NLR helpers and NLRs with integrated domains.
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Affiliation(s)
- E Baggs
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UG, United Kingdom
| | - G Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom
| | - K V Krasileva
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UG, United Kingdom; The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom.
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36
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Losvik A, Beste L, Mehrabi S, Jonsson L. The Protease Inhibitor CI2c Gene Induced by Bird Cherry-Oat Aphid in Barley Inhibits Green Peach Aphid Fecundity in Transgenic Arabidopsis. Int J Mol Sci 2017. [PMID: 28632160 PMCID: PMC5486138 DOI: 10.3390/ijms18061317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aphids are phloem feeders that cause large damage globally as pest insects. They induce a variety of responses in the host plant, but not much is known about which responses are promoting or inhibiting aphid performance. Here, we investigated whether one of the responses induced in barley by the cereal aphid, bird cherry-oat aphid (Rhopalosiphum padi L.) affects aphid performance in the model plant Arabidopsis thaliana L. A barley cDNA encoding the protease inhibitor CI2c was expressed in A. thaliana and aphid performance was studied using the generalist green peach aphid (Myzus persicae Sulzer). There were no consistent effects on aphid settling or preference or on parameters of life span and long-term fecundity. However, short-term tests with apterous adult aphids showed lower fecundity on three of the transgenic lines, as compared to on control plants. This effect was transient, observed on days 5 to 7, but not later. The results suggest that the protease inhibitor is taken up from the tissue during probing and weakly inhibits fecundity by an unknown mechanism. The study shows that a protease inhibitor induced in barley by an essentially monocot specialist aphid can inhibit a generalist aphid in transgenic Arabidopsis.
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Affiliation(s)
| | | | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.
| | - Lisbeth Jonsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.
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37
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Li N, Jia H, Kong Z, Tang W, Ding Y, Liang J, Ma H, Ma Z. Identification and marker-assisted transfer of a new powdery mildew resistance gene at the Pm4 locus in common wheat. MOLECULAR BREEDING 2017; 37:79. [PMID: 0 DOI: 10.1007/s11032-017-0670-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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38
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Zhang ZW, Ma GJ, Zhao J, Markell SG, Qi LL. Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl 19 in confection sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:29-39. [PMID: 27677630 DOI: 10.1007/s00122-016-2786-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/03/2016] [Indexed: 05/20/2023]
Abstract
A new downy mildew resistance gene, Pl 19 , was identified from wild Helianthus annuus accession PI 435414, introduced to confection sunflower, and genetically mapped to linkage group 4 of the sunflower genome. Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC1F2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed that a single dominant gene controls downy mildew resistance in the population. Bulked segregant analysis conducted in the BC1F2 population with 860 simple sequence repeat (SSR) markers indicated that the resistance derived from wild H. annuus was associated with SSR markers located on linkage group (LG) 4 of the sunflower genome. To map and tag this resistance locus, designated Pl 19 , 140 BC1F2 individuals were used to construct a linkage map of the gene region. Two SSR markers, ORS963 and HT298, were linked to Pl 19 within a distance of 4.7 cM. After screening 27 additional single nucleotide polymorphism (SNP) markers previously mapped to this region, two flanking SNP markers, NSA_003564 and NSA_006089, were identified as surrounding the Pl 19 gene at a distance of 0.6 cM from each side. Genetic analysis indicated that Pl 19 is different from Pl 17 , which had previously been mapped to LG4, but is closely linked to Pl 17 . This new gene is highly effective against the most predominant and virulent races of P. halstedii currently identified in North America and is the first downy mildew resistance gene that has been transferred to confection sunflower. The selected resistant germplasm derived from homozygous BC2F3 progeny provides a novel gene for use in confection sunflower breeding programs.
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Affiliation(s)
- Z W Zhang
- Department of Agronomy, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - J Zhao
- Department of Agronomy, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
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Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen. Proc Natl Acad Sci U S A 2016; 113:E6486-E6495. [PMID: 27702901 DOI: 10.1073/pnas.1612947113] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Disease-resistance genes encoding intracellular nucleotide-binding domain and leucine-rich repeat proteins (NLRs) are key components of the plant innate immune system and typically detect the presence of isolate-specific avirulence (AVR) effectors from pathogens. NLR genes define the fastest-evolving gene family of flowering plants and are often arranged in gene clusters containing multiple paralogs, contributing to copy number and allele-specific NLR variation within a host species. Barley mildew resistance locus a (Mla) has been subject to extensive functional diversification, resulting in allelic resistance specificities each recognizing a cognate, but largely unidentified, AVRa gene of the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). We applied a transcriptome-wide association study among 17 Bgh isolates containing different AVRa genes and identified AVRa1 and AVRa13, encoding candidate-secreted effectors recognized by Mla1 and Mla13 alleles, respectively. Transient expression of the effector genes in barley leaves or protoplasts was sufficient to trigger Mla1 or Mla13 allele-specific cell death, a hallmark of NLR receptor-mediated immunity. AVRa1 and AVRa13 are phylogenetically unrelated, demonstrating that certain allelic MLA receptors evolved to recognize sequence-unrelated effectors. They are ancient effectors because corresponding loci are present in wheat powdery mildew. AVRA1 recognition by barley MLA1 is retained in transgenic Arabidopsis, indicating that AVRA1 directly binds MLA1 or that its recognition involves an evolutionarily conserved host target of AVRA1 Furthermore, analysis of transcriptome-wide sequence variation among the Bgh isolates provides evidence for Bgh population structure that is partially linked to geographic isolation.
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Medeiros AH, Mingossi FB, Dias RO, Franco FP, Vicentini R, Mello MO, Moura DS, Silva-Filho MC. Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding. Int J Mol Sci 2016; 17:E1444. [PMID: 27598134 PMCID: PMC5037723 DOI: 10.3390/ijms17091444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/16/2016] [Accepted: 08/25/2016] [Indexed: 11/16/2022] Open
Abstract
Sugarcane's (Saccharum spp.) response to Diatraea saccharalis (F.) (Lepidoptera: (Crambidae) herbivory was investigated using a macroarray spotted with 248 sugarcane Expressed Sequence Tags (ESTs) encoding serine peptidase inhibitors, serine peptidases. and Clp protease system subunits. Our results showed that after nine hours of herbivory, 13 sugarcane genes were upregulated and nine were downregulated. Among the upregulated genes, nine were similar to serine peptidase inhibitors and four were similar to Bowman-Birk Inhibitors (BBIs). Phylogenetic analysis revealed that these sequences belong to a phylogenetic group of sugarcane BBIs that are potentially involved in plant defense against insect predation. The remaining four upregulated genes included serine peptidases and one homolog to the Arabidopsis AAA+ chaperone subunit ClpD, which is a member of the Clp protease system. Among the downregulated genes, five were homologous to serine peptidases and four were homologous to Arabidopsis Clp subunits (three homologous to Clp AAA+ chaperones and one to a ClpP-related ClpR subunit). Although the roles of serine peptidase inhibitors in plant defenses against herbivory have been extensively investigated, the roles of plant serine peptidases and the Clp protease system represent a new and underexplored field of study. The up- and downregulated D. saccharalis genes presented in this study may be candidate genes for the further investigation of the sugarcane response to herbivory.
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Affiliation(s)
- Ane H Medeiros
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, 13600-970 São Paulo, Brazil.
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Fabiana B Mingossi
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Renata O Dias
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Flávia P Franco
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
| | - Renato Vicentini
- Systems Biology Laboratory, Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, 13083-970 São Paulo, Brazil.
| | - Marcia O Mello
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
- Monsanto do Brasil, Campinas, 13069-380 São Paulo, Brazil.
| | - Daniel S Moura
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13400-918 São Paulo, Brazil.
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, 13418-260 São Paulo, Brazil.
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Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas AM. A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL. THE PLANT GENOME 2016; 9. [PMID: 27898833 DOI: 10.3835/plantgenome2015.10.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.
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Andersen EJ, Ali S, Reese RN, Yen Y, Neupane S, Nepal MP. Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). Evol Bioinform Online 2016; 12:99-108. [PMID: 27168720 PMCID: PMC4857794 DOI: 10.4137/ebo.s38085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 11/05/2022] Open
Abstract
Plant disease resistance genes (R-genes) play a critical role in the defense response to pathogens. Barley is one of the most important cereal crops, having a genome recently made available, for which the diversity and evolution of R-genes are not well understood. The main objectives of this research were to conduct a genome-wide identification of barley Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) genes and elucidate their evolutionary history. We employed a Hidden Markov Model using 52 Arabidopsis thaliana CNL reference sequences and analyzed for phylogenetic relationships, structural variation, and gene clustering. We identified 175 barley CNL genes nested into three clades, showing (a) evidence of an expansion of the CNL-C clade, primarily due to tandem duplications; (b) very few members of clade CNL-A and CNL-B; and (c) a complete absence of clade CNL-D. Our results also showed that several of the previously identified mildew locus A (MLA) genes may be allelic variants of two barley CNL genes, MLOC_66581 and MLOC_10425, which respond to powdery mildew. Approximately 23% of the barley CNL genes formed 15 gene clusters located in the extra-pericentromeric regions on six of the seven chromosomes; more than half of the clustered genes were located on chromosomes 1H and 7H. Higher average numbers of exons and multiple splice variants in barley relative to those in Arabidopsis and rice may have contributed to a diversification of the CNL-C members. These results will help us understand the evolution of R-genes with potential implications for developing durable resistance in barley cultivars.
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Affiliation(s)
- Ethan J. Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Shaukat Ali
- Department of Plant Science, South Dakota State University, Brookings, SD, USA
| | - R. Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P. Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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Thomas S, Wahabzada M, Kuska MT, Rascher U, Mahlein AK. Observation of plant-pathogen interaction by simultaneous hyperspectral imaging reflection and transmission measurements. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 44:23-34. [PMID: 32480543 DOI: 10.1071/fp16127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/27/2016] [Indexed: 06/11/2023]
Abstract
Hyperspectral imaging sensors are valuable tools for plant disease detection and plant phenotyping. Reflectance properties are influenced by plant pathogens and resistance responses, but changes of transmission characteristics of plants are less described. In this study we used simultaneously recorded reflectance and transmittance imaging data of resistant and susceptible barley genotypes that were inoculated with Blumeria graminis f. sp. hordei to evaluate the added value of imaging transmission, reflection and absorption for characterisation of disease development. These datasets were statistically analysed using principal component analysis, and compared with visual and molecular disease estimation. Reflection measurement performed significantly better for early detection of powdery mildew infection, colonies could be detected 2 days before symptoms became visible in RGB images. Transmission data could be used to detect powdery mildew 2 days after symptoms becoming visible in reflection based RGB images. Additionally distinct transmission changes occurred at 580-650nm for pixels containing disease symptoms. It could be shown that the additional information of the transmission data allows for a clearer spatial differentiation and localisation between powdery mildew symptoms and necrotic tissue on the leaf then purely reflectance based data. Thus the information of both measurement approaches are complementary: reflectance based measurements facilitate an early detection, and transmission measurements provide additional information to better understand and quantify the complex spatio-temporal dynamics of plant-pathogen interactions.
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Affiliation(s)
- Stefan Thomas
- INRES-Phytomedizin, University Bonn, Nussallee 9, 53115 Bonn, Germany
| | - Mirwaes Wahabzada
- INRES-Phytomedizin, University Bonn, Nussallee 9, 53115 Bonn, Germany
| | | | - Uwe Rascher
- IBG2: Plant Sciences, Forschungszentrum Jülich GMBH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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44
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Dimkpa SON, Lahari Z, Shrestha R, Douglas A, Gheysen G, Price AH. A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1191-200. [PMID: 26552884 PMCID: PMC4753847 DOI: 10.1093/jxb/erv470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus.
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Affiliation(s)
- Stanley O N Dimkpa
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB243UU, UK Current address: Department of Crop and Soil Science, Rivers State University of Science and Technology, Nigeria
| | - Zobaida Lahari
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Roshi Shrestha
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB243UU, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB243UU, UK
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB243UU, UK
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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Amrine KCH, Blanco-Ulate B, Riaz S, Pap D, Jones L, Figueroa-Balderas R, Walker MA, Cantu D. Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew. HORTICULTURE RESEARCH 2015; 2:15037. [PMID: 26504579 PMCID: PMC4591678 DOI: 10.1038/hortres.2015.37] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 05/24/2023]
Abstract
Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study, we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions 'Karadzhandahal', DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.
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Affiliation(s)
- Katherine C H Amrine
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dániel Pap
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - Laura Jones
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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Sekhwal MK, Li P, Lam I, Wang X, Cloutier S, You FM. Disease Resistance Gene Analogs (RGAs) in Plants. Int J Mol Sci 2015; 16:19248-90. [PMID: 26287177 PMCID: PMC4581296 DOI: 10.3390/ijms160819248] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/01/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022] Open
Abstract
Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.
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Affiliation(s)
- Manoj Kumar Sekhwal
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Pingchuan Li
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Irene Lam
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Xiue Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sylvie Cloutier
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Plant Science Department, University of Manitoba, Winnipeg, MB R3T 2N6, Canada.
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Liang Y, Zhang DY, Ouyang S, Xie J, Wu Q, Wang Z, Cui Y, Lu P, Zhang D, Liu ZJ, Zhu J, Chen YX, Zhang Y, Luo MC, Dvorak J, Huo N, Sun Q, Gu YQ, Liu Z. Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1617-29. [PMID: 25993896 DOI: 10.1007/s00122-015-2536-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/02/2015] [Indexed: 05/12/2023]
Abstract
Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.
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Affiliation(s)
- Yong Liang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
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Singh RP, Hodson DP, Jin Y, Lagudah ES, Ayliffe MA, Bhavani S, Rouse MN, Pretorius ZA, Szabo LJ, Huerta-Espino J, Basnet BR, Lan C, Hovmøller MS. Emergence and Spread of New Races of Wheat Stem Rust Fungus: Continued Threat to Food Security and Prospects of Genetic Control. PHYTOPATHOLOGY 2015; 105:872-84. [PMID: 26120730 DOI: 10.1094/phyto-01-15-0030-fi] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the 'Digalu' and 'Robin' varieties in Ethiopia and Kenya, respectively. Enhanced research in the last decade under the umbrella of the Borlaug Global Rust Initiative has identified various race-specific resistance genes that can be utilized, preferably in combinations, to develop resistant varieties. Research and development of improved wheat germplasm with complex adult plant resistance (APR) based on multiple slow-rusting genes has also progressed. Once only the Sr2 gene was known to confer slow rusting APR; now, four more genes-Sr55, Sr56, Sr57, and Sr58-have been characterized and additional quantitative trait loci identified. Cloning of some rust resistance genes opens new perspectives on rust control in the future through the development of multiple resistance gene cassettes. However, at present, disease-surveillance-based chemical control, large-scale deployment of new varieties with multiple race-specific genes or adequate levels of APR, and reducing the cultivation of susceptible varieties in rust hot-spot areas remains the best stem rust management strategy.
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Affiliation(s)
- Ravi P Singh
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - David P Hodson
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Yue Jin
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Evans S Lagudah
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Michael A Ayliffe
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Sridhar Bhavani
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Matthew N Rouse
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Zacharias A Pretorius
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Les J Szabo
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Julio Huerta-Espino
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Bhoja R Basnet
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Caixia Lan
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Mogens S Hovmøller
- First, eleventh, and twelfth authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal, 6-641, 06600, Mexico, D.F.; second author: CIMMYT, Addis Ababa, Ethiopia; third, seventh, and ninth authors: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, University of Minnesota, St. Paul 55108; fourth and fifth authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Agriculture Flagship, GPO Box 1600, Canberra, ACT, 2601, Australia; sixth author: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; eighth author: University of the Free State, Bloemfontein 9300, South Africa; tenth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo de México, México; and thirteenth author: Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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Keller B, Manzanares C, Jara C, Lobaton JD, Studer B, Raatz B. Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:813-26. [PMID: 25740562 PMCID: PMC4544502 DOI: 10.1007/s00122-015-2472-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/31/2015] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection. Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80%. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1(GS, UC) for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75% of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.
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Affiliation(s)
- Beat Keller
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Chloe Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Carlos Jara
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
| | - Juan David Lobaton
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Bodo Raatz
- Agrobiodiversity Research Area, Bean Program, CIAT Cali-Palmira, A. A. 6713, Cali, Colombia
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