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Wu Y, Ma X, Pan Z, Kale SD, Song Y, King H, Zhang Q, Presley C, Deng X, Wei CI, Xiao S. Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew. BMC Genomics 2018; 19:705. [PMID: 30253736 PMCID: PMC6156980 DOI: 10.1186/s12864-018-5069-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici. RESULTS We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification. CONCLUSIONS Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.
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Affiliation(s)
- Ying Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xianfeng Ma
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, 410128 China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiv D. Kale
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Yi Song
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Harlan King
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Qiong Zhang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Christian Presley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cheng-I Wei
- College of Agriculture & Natural Resources, University of Maryland, College Park, MD 20742 USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
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Marchal C, Zhang J, Zhang P, Fenwick P, Steuernagel B, Adamski NM, Boyd L, McIntosh R, Wulff BBH, Berry S, Lagudah E, Uauy C. BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. NATURE PLANTS 2018; 4:662-668. [PMID: 30150615 DOI: 10.1038/s41477-018-0236-4] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/31/2018] [Indexed: 05/13/2023]
Abstract
Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security1. Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)2. This highlights the need to (1) identify genes that, alone or in combination, provide broad-spectrum resistance, and (2) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterization of three major yellow rust resistance genes (Yr7, Yr5 and YrSP) from hexaploid wheat (Triticum aestivum), each having a distinct recognition specificity. We show that Yr5, which remains effective to a broad range of Pst isolates worldwide, is closely related yet distinct from Yr7, whereas YrSP is a truncated version of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain3 that is distinct from those found in non-NLR wheat proteins. We developed diagnostic markers to accelerate haplotype analysis and for marker-assisted selection to expedite the stacking of the non-allelic Yr genes. Our results provide evidence that the BED-NLR gene architecture can provide effective field-based resistance to important fungal diseases such as wheat yellow rust.
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Affiliation(s)
| | - Jianping Zhang
- University of Sydney, Plant Breeding Institute, Cobbitty, New South Wales, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture & Food, Canberra, Australian Capital Territory, Australia
- Henan Tianmin Seed Company Limited, Lankao County, Henan Province, China
| | - Peng Zhang
- University of Sydney, Plant Breeding Institute, Cobbitty, New South Wales, Australia
| | - Paul Fenwick
- Limagrain UK Ltd, Rothwell, Market Rasen, Lincolnshire, UK
| | | | | | - Lesley Boyd
- National Institute of Agricultural Botany (NIAB), Cambridge, UK
| | - Robert McIntosh
- University of Sydney, Plant Breeding Institute, Cobbitty, New South Wales, Australia
| | | | - Simon Berry
- Limagrain UK Ltd, Rothwell, Market Rasen, Lincolnshire, UK
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture & Food, Canberra, Australian Capital Territory, Australia
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53
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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54
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De la Concepcion JC, Franceschetti M, Maqbool A, Saitoh H, Terauchi R, Kamoun S, Banfield MJ. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. NATURE PLANTS 2018; 4:576-585. [PMID: 29988155 DOI: 10.1038/s41477-018-0194-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Accelerated adaptive evolution is a hallmark of plant-pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.
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Affiliation(s)
| | - Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hiromasa Saitoh
- Laboratory of Plant Symbiotic and Parasitic Microbes, Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
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55
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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56
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Haghdoust R, Singh D, Garnica DP, Park RF, Dracatos PM. Isolate Specificity and Polygenic Inheritance of Resistance in Barley to Diverse Heterologous Puccinia striiformis Isolates. PHYTOPATHOLOGY 2018; 108:617-626. [PMID: 29271300 DOI: 10.1094/phyto-10-17-0345-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Barley is a host to Puccinia striiformis f. sp. hordei, and is an intermediate or near nonhost to the formae speciales adapted to wheat (P. striiformis f. sp. tritici) and to barley grass (P. striiformis f. sp. pseudo-hordei). The genetic basis of resistance to these forms of P. striiformis is not well understood. Accordingly, a recombinant inbred line (RIL) population was developed using a P. striiformis-susceptible accession (Biosaline-19) and the immune cultivar Pompadour. We investigated the genetic basis of resistance to four diverse P. striiformis isolates (P. striiformis f. sp. pseudo-hordei, and P. striiformis f. sp. tritici pathotypes 104 E137 A-, 134 E16 A+, and 64 E0 A-). and determined that the immunity in Pompadour at the seedling stage to the different P. striiformis isolates was due to quantitative trait loci (QTL) on chromosomes 1H, 3H, 5H, and 7H with both overlapping and distinct specificities. Further histological analysis confirmed the presence of isolate specificity. The RILs were also assessed in the field for resistance to P. striiformis f. sp. pseudo-hordei, P. striiformis f. sp. hordei, and the leaf rust pathogen (P. hordei) to identify pleiotropic QTL loci effective at the adult plant stage and determine whether the leaf rust resistance in Pompadour (Rph20) was also effective to P. striiformis. RILs that were seedling susceptible to P. striiformis f. sp. pseudo-hordei were resistant in the field, implicating the involvement of adult plant resistance (APR). Additional QTLs were identified on chromosome 7H at the same genetic position as Rph23 (APR to leaf rust), suggesting either pleiotropic resistance or the presence of a stripe rust resistance gene closely linked to or allelic with Rph23. Unlike many pleiotropic APR genes identified and isolated in wheat, our data suggest that the Rph20 locus does not confer resistance to the P. striiformis isolates used in this study (P. striiformis f. sp. hordei [χ2 (independence) = 2.47 P > 0.12] and P. striiformis f. sp. pseudo-hordei [χ2 (independence) = 0.42 P > 0.60]).
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Affiliation(s)
- R Haghdoust
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - D Singh
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - D P Garnica
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - R F Park
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - P M Dracatos
- First, second, fourth, and fifth authors: The University of Sydney, Plant Breeding Institute, Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and second author: CSIRO Plant Industries, GPO Box 1600, Canberra, ACT, 2601, Australia
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57
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McNally KE, Menardo F, Lüthi L, Praz CR, Müller MC, Kunz L, Ben‐David R, Chandrasekhar K, Dinoor A, Cowger C, Meyers E, Xue M, Zeng F, Gong S, Yu D, Bourras S, Keller B. Distinct domains of the AVRPM3 A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. THE NEW PHYTOLOGIST 2018; 218:681-695. [PMID: 29453934 PMCID: PMC6175116 DOI: 10.1111/nph.15026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/05/2018] [Indexed: 05/22/2023]
Abstract
Recognition of the AVRPM3A2/F2 avirulence protein from powdery mildew by the wheat PM3A/F immune receptor induces a hypersensitive response after co-expression in Nicotiana benthamiana. The molecular determinants of this interaction and how they shape natural AvrPm3a2/f2 allelic diversity are unknown. We sequenced the AvrPm3a2/f2 gene in a worldwide collection of 272 mildew isolates. Using the natural polymorphisms of AvrPm3a2/f2 as well as sequence information from related gene family members, we tested 85 single-residue-altered AVRPM3A2/F2 variants with PM3A, PM3F and PM3FL456P/Y458H (modified for improved signaling) in Nicotiana benthamiana for effects on recognition. An intact AvrPm3a2/f2 gene was found in all analyzed isolates and the protein variant recognized by PM3A/F occurred globally at high frequencies. Single-residue alterations in AVRPM3A2/F2 mostly disrupted, but occasionally enhanced, the recognition response by PM3A, PM3F and PM3FL456P/Y458H . Residues enhancing hypersensitive responses constituted a protein domain separate from both naturally occurring polymorphisms and positively selected residues of the gene family. These results demonstrate the utility of using gene family sequence diversity to screen residues for their role in recognition. This approach identified a putative interaction surface in AVRPM3A2/F2 not polymorphic in natural alleles. We conclude that molecular mechanisms besides recognition drive AvrPm3a2/f2 diversification.
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Affiliation(s)
- Kaitlin Elyse McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Linda Lüthi
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Lukas Kunz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani Center50250Bet DaganIsrael
| | - Kottakota Chandrasekhar
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Amos Dinoor
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Christina Cowger
- United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)North Carolina State UniversityRaleighNC27695USA
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Emily Meyers
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Mingfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Fangsong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Shuangjun Gong
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
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58
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Boni R, Chauhan H, Hensel G, Roulin A, Sucher J, Kumlehn J, Brunner S, Krattinger SG, Keller B. Pathogen-inducible Ta-Lr34res expression in heterologous barley confers disease resistance without negative pleiotropic effects. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:245-253. [PMID: 28561994 PMCID: PMC5785347 DOI: 10.1111/pbi.12765] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
Plant diseases are a serious threat to crop production. The informed use of naturally occurring disease resistance in plant breeding can greatly contribute to sustainably reduce yield losses caused by plant pathogens. The Ta-Lr34res gene encodes an ABC transporter protein and confers partial, durable, and broad spectrum resistance against several fungal pathogens in wheat. Transgenic barley lines expressing Ta-Lr34res showed enhanced resistance against powdery mildew and leaf rust of barley. While Ta-Lr34res is only active at adult stage in wheat, Ta-Lr34res was found to be highly expressed already at the seedling stage in transgenic barley resulting in severe negative effects on growth. Here, we expressed Ta-Lr34res under the control of the pathogen-inducible Hv-Ger4c promoter in barley. Sixteen independent barley transformants showed strong resistance against leaf rust and powdery mildew. Infection assays and growth parameter measurements were performed under standard glasshouse and near-field conditions using a convertible glasshouse. Two Hv-Ger4c::Ta-Lr34res transgenic events were analysed in detail. Plants of one transformation event had similar grain production compared to wild-type under glasshouse and near-field conditions. Our results showed that negative effects caused by constitutive high expression of Ta-Lr34res driven by the endogenous wheat promoter in barley can be eliminated by inducible expression without compromising disease resistance. These data demonstrate that Ta-Lr34res is agronomically useful in barley. We conclude that the generation of a large number of transformants in different barley cultivars followed by early field testing will allow identifying barley lines suitable for breeding.
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Affiliation(s)
- Rainer Boni
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Harsh Chauhan
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
- Present address:
Department of BiotechnologyIndian Institute of Technology RoorkeeRoorkeeUttarakhand247667India
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenPlant Reproductive BiologySeeland/OT GaterslebenGermany
| | - Anne Roulin
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Justine Sucher
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenPlant Reproductive BiologySeeland/OT GaterslebenGermany
| | | | - Simon G. Krattinger
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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59
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Kuska MT, Brugger A, Thomas S, Wahabzada M, Kersting K, Oerke EC, Steiner U, Mahlein AK. Spectral Patterns Reveal Early Resistance Reactions of Barley Against Blumeria graminis f. sp. hordei. PHYTOPATHOLOGY 2017; 107:1388-1398. [PMID: 28665761 DOI: 10.1094/phyto-04-17-0128-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Differences in early plant-pathogen interactions are mainly characterized by using destructive methods. Optical sensors are advanced techniques for phenotyping host-pathogen interactions on different scales and for detecting subtle plant resistance responses against pathogens. A microscope with a hyperspectral camera was used to study interactions between Blumeria graminis f. sp. hordei and barley (Hordeum vulgare) genotypes with high susceptibility or resistance due to hypersensitive response (HR) and papilla formation. Qualitative and quantitative assessment of pathogen development was used to explain changes in hyperspectral signatures. Within 48 h after inoculation, genotype-specific changes in the green and red range (500 to 690 nm) and a blue shift of the red-edge inflection point were observed. Manual analysis indicated resistance-specific reflectance patterns from 1 to 3 days after inoculation. These changes could be linked to host plant modifications depending on individual host-pathogen interactions. Retrospective analysis of hyperspectral images revealed spectral characteristics of HR against B. graminis f. sp. hordei. For early HR detection, an advanced data mining approach localized HR spots before they became visible on the RGB images derived from hyperspectral imaging. The link among processes during pathogenesis and host resistance to changes in hyperspectral signatures provide evidence that sensor-based phenotyping is suitable to advance time-consuming and cost-expensive visual rating of plant disease resistances.
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Affiliation(s)
- Matheus Thomas Kuska
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Anna Brugger
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Stefan Thomas
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Mirwaes Wahabzada
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Kristian Kersting
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Erich-Christian Oerke
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Ulrike Steiner
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Anne-Katrin Mahlein
- First, second, third, fourth, sixth, seventh, and eighth authors: Institute for Crop Science and Resource Conservation (INRES)-Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; fifth author: CS Department and Centre for Cognitive Science, TU Darmstadt, Hochschulstrasse 1, 64289 Darmstadt, Germany; and eighth author: Institute of Sugar Beet Research (IfZ), Holtenser Landstraße 77, 37079 Göttingen, Germany
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60
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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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61
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Marden JH, Mangan SA, Peterson MP, Wafula E, Fescemyer HW, Der JP, dePamphilis CW, Comita LS. Ecological genomics of tropical trees: how local population size and allelic diversity of resistance genes relate to immune responses, cosusceptibility to pathogens, and negative density dependence. Mol Ecol 2017; 26:2498-2513. [PMID: 28042895 DOI: 10.1111/mec.13999] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023]
Abstract
In tropical forests, rarer species show increased sensitivity to species-specific soil pathogens and more negative effects of conspecific density on seedling survival (NDD). These patterns suggest a connection between ecology and immunity, perhaps because small population size disproportionately reduces genetic diversity of hyperdiverse loci such as immunity genes. In an experiment examining seedling roots from six species in one tropical tree community, we found that smaller populations have reduced amino acid diversity in pathogen resistance (R) genes but not the transcriptome in general. Normalized R gene amino acid diversity varied with local abundance and prior measures of differences in sensitivity to conspecific soil and NDD. After exposure to live soil, species with lower R gene diversity had reduced defence gene induction, more cosusceptibility of maternal cohorts to colonization by potentially pathogenic fungi, reduced root growth arrest (an R gene-mediated response) and their root-associated fungi showed lower induction of self-defence (antioxidants). Local abundance was not related to the ability to induce immune responses when pathogen recognition was bypassed by application of salicylic acid, a phytohormone that activates defence responses downstream of R gene signalling. These initial results support the hypothesis that smaller local tree populations have reduced R gene diversity and recognition-dependent immune responses, along with greater cosusceptibility to species-specific pathogens that may facilitate disease transmission and NDD. Locally rare species may be less able to increase their equilibrium abundance without genetic boosts to defence via immigration of novel R gene alleles from a larger and more diverse regional population.
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Affiliation(s)
- J H Marden
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - S A Mangan
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Smithsonian Tropical Research Institute, República de Panamá, 0843-03092, Panama, Panama
| | - M P Peterson
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - E Wafula
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - H W Fescemyer
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - J P Der
- Department of Biological Science, California State University, Fullerton, CA, 92834, USA
| | - C W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - L S Comita
- Smithsonian Tropical Research Institute, República de Panamá, 0843-03092, Panama, Panama.,School of Forestry and Environmental Studies, Yale University, New Haven, CT, 06511, USA
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62
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Praz CR, Bourras S, Zeng F, Sánchez‐Martín J, Menardo F, Xue M, Yang L, Roffler S, Böni R, Herren G, McNally KE, Ben‐David R, Parlange F, Oberhaensli S, Flückiger S, Schäfer LK, Wicker T, Yu D, Keller B. AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. THE NEW PHYTOLOGIST 2017; 213:1301-1314. [PMID: 27935041 PMCID: PMC5347869 DOI: 10.1111/nph.14372] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 05/20/2023]
Abstract
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3a2/f2 that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2. The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase-like effectors, including Avra13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13. These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Fansong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | | | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Lijun Yang
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Stefan Roffler
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Rainer Böni
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Gerard Herren
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Kaitlin E. McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani CenterBet Dagan50250Israel
| | - Francis Parlange
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Luisa K. Schäfer
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins. Proc Natl Acad Sci U S A 2016; 113:12856-12861. [PMID: 27791121 DOI: 10.1073/pnas.1609922113] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Plants use intracellular immunity receptors, known as nucleotide-binding oligomerization domain-like receptors (NLRs), to recognize specific pathogen effector proteins and induce immune responses. These proteins provide resistance to many of the world's most destructive plant pathogens, yet we have a limited understanding of the molecular mechanisms that lead to defense signaling. We examined the wheat NLR protein, Sr33, which is responsible for strain-specific resistance to the wheat stem rust pathogen, Puccinia graminis f. sp. tritici We present the solution structure of a coiled-coil (CC) fragment from Sr33, which adopts a four-helix bundle conformation. Unexpectedly, this structure differs from the published dimeric crystal structure of the equivalent region from the orthologous barley powdery mildew resistance protein, MLA10, but is similar to the structure of the distantly related potato NLR protein, Rx. We demonstrate that these regions are, in fact, largely monomeric and adopt similar folds in solution in all three proteins, suggesting that the CC domains from plant NLRs adopt a conserved fold. However, larger C-terminal fragments of Sr33 and MLA10 can self-associate both in vitro and in planta, and this self-association correlates with their cell death signaling activity. The minimal region of the CC domain required for both cell death signaling and self-association extends to amino acid 142, thus including 22 residues absent from previous biochemical and structural protein studies. These data suggest that self-association of the minimal CC domain is necessary for signaling but is likely to involve a different structural basis than previously suggested by the MLA10 crystallographic dimer.
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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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Krattinger SG, Keller B. Molecular genetics and evolution of disease resistance in cereals. THE NEW PHYTOLOGIST 2016; 212:320-32. [PMID: 27427289 DOI: 10.1111/nph.14097] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 05/02/2023]
Abstract
Contents 320 I. 320 II. 321 III. 321 IV. 322 V. 324 VI. 328 VII. 329 330 References 330 SUMMARY: Cereal crops produce a large part of the globally consumed food and feed. Because of the constant presence of devastating pathogens, the molecular characterization of disease resistance is a major research area and highly relevant for breeding. There has been recent and accelerating progress in the understanding of three distinct resistance mechanisms in cereals: resistance conferred by plasma membrane-localized receptor proteins; race-specific resistance conferred by intracellular immune receptors; and quantitative disease resistance. Intracellular immune receptors provide a particularly rich source for evolutionary studies, and have, for example, resulted in the recent discovery of a novel detection mechanism based on integrated decoy domains. Evolutionary studies have also revealed the origins of active resistance genes in both wild progenitors of today's cereals as well as in cultivated forms. In addition, independent evolution of orthologous genes in related cereals has resulted in resistance to different pathogen species. Quantitative resistance genes have been best characterized in wheat. The quantitative resistance genes identified so far in wheat encode transporter proteins or unusual kinase proteins. The recent discoveries in these three different resistance mechanisms have contributed to the basic molecular understanding of cereal immunity against pathogens and have suggested novel applications for resistance breeding.
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Affiliation(s)
- Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
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66
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Cesari S, Moore J, Chen C, Webb D, Periyannan S, Mago R, Bernoux M, Lagudah ES, Dodds PN. Cytosolic activation of cell death and stem rust resistance by cereal MLA-family CC-NLR proteins. Proc Natl Acad Sci U S A 2016; 113:10204-9. [PMID: 27555587 PMCID: PMC5018743 DOI: 10.1073/pnas.1605483113] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Plants possess intracellular immune receptors designated "nucleotide-binding domain and leucine-rich repeat" (NLR) proteins that translate pathogen-specific recognition into disease-resistance signaling. The wheat immune receptors Sr33 and Sr50 belong to the class of coiled-coil (CC) NLRs. They confer resistance against a broad spectrum of field isolates of Puccinia graminis f. sp. tritici, including the Ug99 lineage, and are homologs of the barley powdery mildew-resistance protein MLA10. Here, we show that, similarly to MLA10, the Sr33 and Sr50 CC domains are sufficient to induce cell death in Nicotiana benthamiana Autoactive CC domains and full-length Sr33 and Sr50 proteins self-associate in planta In contrast, truncated CC domains equivalent in size to an MLA10 fragment for which a crystal structure was previously determined fail to induce cell death and do not self-associate. Mutations in the truncated region also abolish self-association and cell-death signaling. Analysis of Sr33 and Sr50 CC domains fused to YFP and either nuclear localization or nuclear export signals in N benthamiana showed that cell-death induction occurs in the cytosol. In stable transgenic wheat plants, full-length Sr33 proteins targeted to the cytosol provided rust resistance, whereas nuclear-targeted Sr33 was not functional. These data are consistent with CC-mediated induction of both cell-death signaling and stem rust resistance in the cytosolic compartment, whereas previous research had suggested that MLA10-mediated cell-death and disease resistance signaling occur independently, in the cytosol and nucleus, respectively.
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Affiliation(s)
- Stella Cesari
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - John Moore
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Daryl Webb
- Centre for Advanced Microscopy, Australian National University, Canberra, ACT 0200, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization Agriculture, Canberra, ACT 2601, Australia;
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67
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Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib. FRONTIERS IN PLANT SCIENCE 2016; 7:915. [PMID: 27446145 PMCID: PMC4917536 DOI: 10.3389/fpls.2016.00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level.
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Affiliation(s)
- Kumar Vasudevan
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
| | | | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
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68
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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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Stuttmann J, Peine N, Garcia AV, Wagner C, Choudhury SR, Wang Y, James GV, Griebel T, Alcázar R, Tsuda K, Schneeberger K, Parker JE. Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genet 2016; 12:e1005990. [PMID: 27082651 PMCID: PMC4833295 DOI: 10.1371/journal.pgen.1005990] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways. Plants tune their cellular and developmental programs to different environmental stimuli. Central players in the plant biotic stress response network are intracellular NLR receptors which intercept specific disease-inducing molecules (effectors) produced by pathogenic microbes. Variation in NLR gene repertoires between plant genetic lines is driven by pathogen selection pressure. One evolutionary question is how new, functional NLRs are assembled within a plant genome without mis-activating defense pathways, which can have strong negative effects on growth and fitness. This study focuses on a large, polymorphic sub-class of NLR receptors called TNLs present in dicotyledenous plant lineages. TNL receptors confer immunity to a broad range of pathogens. They also frequently underlie autoimmunity caused by their mis-regulation or deleterious allelic interactions with other genes in crosses between different genetic lines (hybrid incompatibility, HI). TNL pathogen-triggered and autoimmune responses require the conserved nucleocytoplasmic protein EDS1 to transcriptionally reprogram cells for defense. We discover in Arabidopsis thaliana that high levels of nuclear-enriched EDS1 induce transcriptional activation of defenses and growth inhibition without a pathogen effector stimulus. In a mutational screen, we identify one rapidly evolving TNL gene, DM2hLer, as a driver of nuclear EDS1 autoimmunity. DM2hLer also contributes to two separate cases of EDS1-dependent autoimmunity. Genetic cooperation between DM2hLer and EDS1 suggests a functional relationship in the transcriptional feed-forward regulation of defense pathways.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
- * E-mail: (JS); (JEP)
| | - Nora Peine
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana V. Garcia
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christine Wagner
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Sayan R. Choudhury
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yiming Wang
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Griebel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Alcázar
- Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (JS); (JEP)
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70
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Dawson AM, Ferguson JN, Gardiner M, Green P, Hubbard A, Moscou MJ. Isolation and fine mapping of Rps6: an intermediate host resistance gene in barley to wheat stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:831-843. [PMID: 26754419 PMCID: PMC4799244 DOI: 10.1007/s00122-015-2659-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/14/2015] [Indexed: 05/24/2023]
Abstract
We uncouple host and nonhost resistance in barley to Puccinia striiformis ff. spp. hordei and tritici . We isolate, fine map, and physically anchor Rps6 to chromosome 7H in barley. A plant may be considered a nonhost of a pathogen if all known genotypes of a plant species are resistant to all known isolates of a pathogen species. However, if a small number of genotypes are susceptible to some known isolates of a pathogen species this plant may be considered an intermediate host. Barley (Hordeum vulgare) is an intermediate host for Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. We wanted to understand the genetic architecture underlying resistance to Pst and to determine whether any overlap exists with resistance to the host pathogen, Puccinia striiformis f. sp. hordei (Psh). We mapped Pst resistance to chromosome 7H and show that host and intermediate host resistance is genetically uncoupled. Therefore, we designate this resistance locus Rps6. We used phenotypic and genotypic selection on F2:3 families to isolate Rps6 and fine mapped the locus to a 0.1 cM region. Anchoring of the Rps6 locus to the barley physical map placed the region on a single fingerprinted contig spanning a physical region of 267 kb. Efforts are now underway to sequence the minimal tiling path and to delimit the physical region harboring Rps6. This will facilitate additional marker development and permit identification of candidate genes in the region.
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Affiliation(s)
- Andrew M Dawson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - John N Ferguson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Matthew Gardiner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Phon Green
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amelia Hubbard
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Matthew J Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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71
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Parrott DL, Huang L, Fischer AM. Downregulation of a barley (Hordeum vulgare) leucine-rich repeat, non-arginine-aspartate receptor-like protein kinase reduces expression of numerous genes involved in plant pathogen defense. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 100:130-140. [PMID: 26820571 DOI: 10.1016/j.plaphy.2016.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/12/2016] [Indexed: 05/24/2023]
Abstract
Pattern recognition receptors represent a first line of plant defense against pathogens. Comparing the flag leaf transcriptomes of barley (Hordeum vulgare L.) near-isogenic lines varying in the allelic state of a locus controlling senescence, we have previously identified a leucine-rich repeat receptor-like protein kinase gene (LRR-RLK; GenBank accession: AK249842), which was strongly upregulated in leaves of early-as compared to late-senescing germplasm. Bioinformatic analysis indicated that this gene codes for a subfamily XII, non-arginine-aspartate (non-RD) LRR-RLK. Virus-induced gene silencing resulted in a two-fold reduction of transcript levels as compared to controls. Transcriptomic comparison of leaves from untreated plants, from plants treated with virus only without any plant sequences (referred to as 'empty virus' control), and from plants in which AK249842 expression was knocked down identified numerous genes involved in pathogen defense. These genes were strongly induced in 'empty virus' as compared to untreated controls, but their expression was significantly reduced (again compared to 'empty virus' controls) when AK249842 was knocked down, indicating that their expression partially depends on the LRR-RLK investigated here. Expression analysis, using datasets from BarleyBase/PLEXdb, demonstrated that AK249842 transcript levels are heavily influenced by the allelic state of the well-characterized mildew resistance a (Mla) locus, and that the gene is induced after powdery mildew and stem rust infection. Together, our data suggest that AK249842 is a barley pattern recognition receptor with a tentative role in defense against fungal pathogens, setting the stage for its full functional characterization.
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Affiliation(s)
- David L Parrott
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Andreas M Fischer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA.
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72
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Bourras S, McNally KE, Müller MC, Wicker T, Keller B. Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0. FRONTIERS IN PLANT SCIENCE 2016; 7:241. [PMID: 26973683 PMCID: PMC4771761 DOI: 10.3389/fpls.2016.00241] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/12/2016] [Indexed: 05/22/2023]
Abstract
The gene-for-gene hypothesis states that for each gene controlling resistance in the host, there is a corresponding, specific gene controlling avirulence in the pathogen. Allelic series of the cereal mildew resistance genes Pm3 and Mla provide an excellent system for genetic and molecular analysis of resistance specificity. Despite this opportunity for molecular research, avirulence genes in mildews remain underexplored. Earlier work in barley powdery mildew (B.g. hordei) has shown that the reaction to some Mla resistance alleles is controlled by multiple genes. Similarly, several genes are involved in the specific interaction of wheat mildew (B.g. tritici) with the Pm3 allelic series. We found that two mildew genes control avirulence on Pm3f: one gene is involved in recognition by the resistance protein as demonstrated by functional studies in wheat and the heterologous host Nicotiana benthamiana. A second gene is a suppressor, and resistance is only observed in mildew genotypes combining the inactive suppressor and the recognized Avr. We propose that such suppressor/avirulence gene combinations provide the basis of specificity in mildews. Depending on the particular gene combinations in a mildew race, different genes will be genetically identified as the "avirulence" gene. Additionally, the observation of two LINE retrotransposon-encoded avirulence genes in B.g. hordei further suggests that the control of avirulence in mildew is more complex than a canonical gene-for-gene interaction. To fully understand the mildew-cereal interactions, more knowledge on avirulence determinants is needed and we propose ways how this can be achieved based on recent advances in the field.
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73
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Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo MC, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y, Ayliffe MA, Bariana H, Park RF, McIntosh R, Doležel J, Bergès H, Spielmeyer W, Lagudah ES, Ellis JG, Dodds PN. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. NATURE PLANTS 2015; 1:15186. [PMID: 27251721 DOI: 10.1038/nplants.2015.186] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 05/18/2023]
Abstract
We identify the wheat stem rust resistance gene Sr50 (using physical mapping, mutation and complementation) as homologous to barley Mla, encoding a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity different from Sr31 and other genes on rye chromosome 1RS, and is effective against the broadly virulent Ug99 race lineage. Extensive haplotype diversity at the rye Sr50 locus holds promise for mining effective resistance genes.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Sonia Vautrin
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Urmil Bansal
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Matthew Rouse
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Haydar Karaoglu
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | | | - James Kolmer
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Yue Jin
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | | | - Harbans Bariana
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert F Park
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert McIntosh
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Hélène Bergès
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | | | - Evans S Lagudah
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Jeff G Ellis
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peter N Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
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74
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Identification of novel alleles of the rice blast resistance gene Pi54. Sci Rep 2015; 5:15678. [PMID: 26498172 PMCID: PMC4620502 DOI: 10.1038/srep15678] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 10/01/2015] [Indexed: 12/13/2022] Open
Abstract
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.
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75
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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: 192] [Impact Index Per Article: 21.3] [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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Gao D, Appiano M, Huibers RP, Loonen AEHM, Visser RGF, Wolters AMA, Bai Y. Natural loss-of-function mutation of EDR1 conferring resistance to tomato powdery mildew in Arabidopsis thaliana accession C24. MOLECULAR PLANT PATHOLOGY 2015; 16:71-82. [PMID: 24925473 PMCID: PMC6638503 DOI: 10.1111/mpp.12165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To screen for potentially novel types of resistance to tomato powdery mildew Oidium neolycopersici, a disease assay was performed on 123 Arabidopsis thaliana accessions. Forty accessions were fully resistant, and one, C24, was analysed in detail. By quantitative trait locus (QTL) analysis of an F2 population derived from C24 × Sha (susceptible accession), two QTLs associated with resistance were identified in C24. Fine mapping of QTL-1 on chromosome 1 delimited the region to an interval of 58 kb encompassing 15 candidate genes. One of these was Enhanced Disease Resistance 1 (EDR1). Evaluation of the previously obtained edr1 mutant of Arabidopsis accession Col-0, which was identified because of its resistance to powdery mildew Golovinomyces cichoracearum, showed that it also displayed resistance to O. neolycopersici. Sequencing of EDR1 in our C24 germplasm (referred to as C24-W) revealed two missing nucleotides in the second exon of EDR1 resulting in a premature stop codon. Remarkably, C24 obtained from other laboratories does not contain the EDR1 mutation. To verify the identity of C24-W, a DNA region containing a single nucleotide polymorphism (SNP) unique to C24 was sequenced showing that C24-W contains the C24-specific nucleotide. C24-W showed enhanced resistance to O. neolycopersici compared with C24 not containing the edr1 mutation. Furthermore, C24-W displayed a dwarf phenotype, which was not associated with the mutation in EDR1 and was not caused by the differential accumulation of pathogenesis-related genes. In conclusion, we identified a natural edr1 mutant in the background of C24.
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Affiliation(s)
- Dongli Gao
- Wageningen UR Plant Breeding, Wageningen University, Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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77
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Friesen ML, von Wettberg EJB, Badri M, Moriuchi KS, Barhoumi F, Chang PL, Cuellar-Ortiz S, Cordeiro MA, Vu WT, Arraouadi S, Djébali N, Zribi K, Badri Y, Porter SS, Aouani ME, Cook DR, Strauss SY, Nuzhdin SV. The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula. BMC Genomics 2014; 15:1160. [PMID: 25534372 PMCID: PMC4410866 DOI: 10.1186/1471-2164-15-1160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress. Results Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape. Conclusions This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1160) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maren L Friesen
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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78
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Liu J, Cheng X, Liu D, Xu W, Wise R, Shen QH. The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling. PLoS Genet 2014; 10:e1004755. [PMID: 25502438 PMCID: PMC4263374 DOI: 10.1371/journal.pgen.1004755] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 09/15/2014] [Indexed: 01/19/2023] Open
Abstract
Barley (Hordeum vulgare L.) Mla alleles encode coiled-coil (CC), nucleotide binding, leucine-rich repeat (NB-LRR) receptors that trigger isolate-specific immune responses against the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). How Mla or NB-LRR genes in grass species are regulated at post-transcriptional level is not clear. The microRNA family, miR9863, comprises four members that differentially regulate distinct Mla alleles in barley. We show that miR9863 members guide the cleavage of Mla1 transcripts in barley, and block or reduce the accumulation of MLA1 protein in the heterologous Nicotiana benthamiana expression system. Regulation specificity is determined by variation in a unique single-nucleotide-polymorphism (SNP) in mature miR9863 family members and two SNPs in the Mla miR9863-binding site that separates these alleles into three groups. Further, we demonstrate that 22-nt miR9863s trigger the biogenesis of 21-nt phased siRNAs (phasiRNAs) and together these sRNAs form a feed-forward regulation network for repressing the expression of group I Mla alleles. Overexpression of miR9863 members specifically attenuates MLA1, but not MLA10-triggered disease resistance and cell-death signaling. We propose a key role of the miR9863 family in dampening immune response signaling triggered by a group of MLA immune receptors in barley. Plants rely on cell-surface and intracellular immune receptors to sense pathogen invasion and to mediate defense responses. However, uncontrolled activation of immune responses is harmful to plant growth and development. Small RNAs have recently been shown to fine-tune the expression of intracellular immune receptors and contribute to the regulation of defense signaling in dicot plants, while similar processes have not been well documented in monocot grain crops, such as barley and wheat. Here, we show that, in barley, some members of the miR9863 family target a subset of Mla alleles that confer race-specific disease resistance to the powdery mildew fungus. These miRNAs act on Mla transcripts by cleavage and translational repression. Production of a type of trans-acting small RNAs, designated as phasiRNAs, enhances the effects of miRNA regulation on Mla targets. We propose that Mla-mediated immune signaling is fine-tuned by the miRNAs at later stage of MLA activation to avoid overloading of immune responses in barley cells.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiliu Cheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Da Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weihui Xu
- Department of Plant Pathology & Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa, United States of America
| | - Roger Wise
- Department of Plant Pathology & Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa, United States of America
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, United States of America
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Centre for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Dogimont C, Chovelon V, Pauquet J, Boualem A, Bendahmane A. The Vat locus encodes for a CC-NBS-LRR protein that confers resistance to Aphis gossypii infestation and A. gossypii-mediated virus resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:993-1004. [PMID: 25283874 DOI: 10.1111/tpj.12690] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 05/06/2023]
Abstract
Aphis gossypii is a polyphagous sucking aphid and a vector for many viruses. In Cucumis melo, a dominant locus, Vat, confers a high level of resistance to Aphis gossypii infestation and to viruses transmitted by this vector. To investigate the mechanism underlying this double resistance, we first genetically dissected the Vat locus. We delimited the double resistance to a single gene that encodes for a coiled-coil-nucleotide-binding-site-leucine-rich repeat (CC-NBS-LRR) protein type. To validate the genetic data, transgenic lines expressing the Vat gene were generated and assessed for the double resistance. In this analysis, Vat-transgenic plants were resistant to A. gossypii infestation as well as A. gossypii-mediated virus transmission. When the plants were infected mechanically, virus infection occurred on both transgenic and non-transgenic control plants. These results confirmed that the cloned CC-NBS-LRR gene mediates both resistance to aphid infestation and virus infection using A. gossypii as a vector. This resistance also invokes a separate recognition and response phases in which the recognition phase involves the interaction of an elicitor molecule from the aphid and Vat from the plant. The response phase is not specific and blocks both aphid infestation and virus infection. Sequence analysis of Vat alleles suggests a major role of an unusual conserved LRR repeat in the recognition of A. gossypii.
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Affiliation(s)
- Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, BP 94, F-84143, Montfavet, France
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80
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Sela H, Spiridon LN, Ashkenazi H, Bhullar NK, Brunner S, Petrescu AJ, Fahima T, Keller B, Jordan T. Three-dimensional modeling and diversity analysis reveals distinct AVR recognition sites and evolutionary pathways in wild and domesticated wheat Pm3 R genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:835-45. [PMID: 24742072 DOI: 10.1094/mpmi-01-14-0009-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Pm3 gene confers resistance against wheat powdery mildew. Studies of Pm3 diversity have shown that Pm3 alleles isolated from southern populations of wild emmer wheat located in Lebanon, Jordan, Israel, and Syria are more diverse and more distant from bread wheat alleles than alleles from the northern wild wheat populations located in Turkey, Iran, and Iraq. Therefore, southern populations from Israel were studied extensively to reveal novel Pm3 alleles that are absent from the cultivated gene pool. Candidate Pm3 genes were isolated via a polymerase chain reaction cloning approach. Known and newly identified Pm3 genes were subjected to variation analysis and polymorphic amino acid residues were superimposed on a three-dimensional (3D) model of PM3. The region of highest interspecies diversity between Triticum aestivum and T. dicoccoides lies in leucine-rich repeats (LRR) 19 to 24, whereas most intraspecies diversity in T. aestivum is located in LRR 25 to 28. Interestingly, these two regions are separated by one large LRR whose propensity for flexibility facilitates the conformation of the PM3 LRR domain into two differently structured models. The combination of evolutionary and protein 3D structure analysis revealed that Pm3 genes in wild and domesticated wheat show different evolutionary histories which might have been triggered through different interactions with the powdery mildew pathogen.
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81
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Xu W, Meng Y, Wise RP. Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. THE NEW PHYTOLOGIST 2014; 201:1396-1412. [PMID: 24246006 DOI: 10.1111/nph.12598] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/08/2013] [Indexed: 05/07/2023]
Abstract
• Barley (Hordeum vulgare L.) Mildew resistance locus a (Mla) confers allele-specific interactions with natural variants of the ascomycete fungus Blumeria graminis f. sp. hordei (Bgh), the causal agent of powdery mildew disease. Significant reprogramming of Mla-mediated gene expression occurs upon infection by this obligate biotrophic pathogen. • We utilized a proteomics-based approach, combined with barley mla, required for Mla12 resistance1 (rar1), and restoration of Mla resistance1 (rom1) mutants, to identify components of Mla-directed signaling. • Loss-of-function mutations in Mla and Rar1 both resulted in the reduced accumulation of chloroplast copper/zinc superoxide dismutase 1 (HvSOD1), whereas loss of function in Rom1 re-established HvSOD1 levels. In addition, both Mla and Rom1 negatively regulated hvu-microRNA398 (hvu-miR398), and up-regulation of miR398 was coupled to reduced HvSOD1 expression. Barley stripe mosaic virus (BSMV)-mediated over-expression of both barley and Arabidopsis miR398 repressed accumulation of HvSOD1, and BSMV-induced gene silencing of HvSod1 impeded Mla-triggered H₂O₂ and hypersensitive reaction (HR) at barley-Bgh interaction sites. • These data indicate that Mla- and Rom1-regulated hvu-miR398 represses HvSOD1 accumulation, influencing effector-induced HR in response to the powdery mildew fungus.
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Affiliation(s)
- Weihui Xu
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
| | - Yan Meng
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
| | - Roger P Wise
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA, 50011-1020, USA
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Iowa State University, Ames, IA, 50011-1020, USA
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Hurni S, Brunner S, Buchmann G, Herren G, Jordan T, Krukowski P, Wicker T, Yahiaoui N, Mago R, Keller B. Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:957-69. [PMID: 24124925 DOI: 10.1111/tpj.12345] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/25/2013] [Accepted: 10/04/2013] [Indexed: 05/18/2023]
Abstract
The improvement of wheat through breeding has relied strongly on the use of genetic material from related wild and domesticated grass species. The 1RS chromosome arm from rye was introgressed into wheat and crossed into many wheat lines, as it improves yield and fungal disease resistance. Pm8 is a powdery mildew resistance gene on 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Here we show by homology-based cloning and subsequent physical and genetic mapping that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. These results show that the two genes have evolved independently after the divergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes. This suggests that they recognize directly or indirectly the same pathogen effectors that have been conserved in the powdery mildews of wheat and rye.
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Affiliation(s)
- Severine Hurni
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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83
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Chang C, Zhang L, Shen QH. Partitioning, repressing and derepressing: dynamic regulations in MLA immune receptor triggered defense signaling. FRONTIERS IN PLANT SCIENCE 2013; 4:396. [PMID: 24115952 PMCID: PMC3792363 DOI: 10.3389/fpls.2013.00396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/16/2013] [Indexed: 05/09/2023]
Abstract
Plants and animals have evolved intracellular nucleotide-binding domain and leucine-rich repeat-containing immune receptors (NLRs) to perceive non-self and trigger immune responses. Plant NLRs detect strain-specific pathogen effectors and activate immune signaling leading to extensive transcriptional reprogramming and termination of pathogen infection. Here we review the recent findings in barley MLA immune receptor mediated immune responses against the barley powdery mildew fungus. We focus on nucleocytoplasmic partitioning of immune receptor, bifurcation of immune signaling, transcriptional repression and derepression connecting receptor activation to immune responses. We also discuss similar findings from other plant NLRs where appropriate.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Ling Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- *Correspondence: Qian-Hua Shen, State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China e-mail:
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84
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Jacob F, Vernaldi S, Maekawa T. Evolution and Conservation of Plant NLR Functions. Front Immunol 2013; 4:297. [PMID: 24093022 PMCID: PMC3782705 DOI: 10.3389/fimmu.2013.00297] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/09/2013] [Indexed: 12/21/2022] Open
Abstract
In plants and animals, nucleotide-binding domain and leucine-rich repeats (NLR)-containing proteins play pivotal roles in innate immunity. Despite their similar biological functions and protein architecture, comparative genome-wide analyses of NLRs and genes encoding NLR-like proteins suggest that plant and animal NLRs have independently arisen in evolution. Furthermore, the demonstration of interfamily transfer of plant NLR functions from their original species to phylogenetically distant species implies evolutionary conservation of the underlying immune principle across plant taxonomy. In this review we discuss plant NLR evolution and summarize recent insights into plant NLR-signaling mechanisms, which might constitute evolutionarily conserved NLR-mediated immune mechanisms.
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Affiliation(s)
- Florence Jacob
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research , Cologne , Germany ; Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d'Essone , Evry , France
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85
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Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, McIntosh R, Dodds P, Dvorak J, Lagudah E. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 2013; 341:786-8. [PMID: 23811228 DOI: 10.1126/science.1239028] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.
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Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT 2601, Australia
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86
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Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, Ver Loren van Themaat E. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 2013; 110:E2219-28. [PMID: 23696672 PMCID: PMC3683789 DOI: 10.1073/pnas.1306807110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barley powdery mildew, Blumeria graminis f. sp. hordei (Bgh), is an obligate biotrophic ascomycete fungal pathogen that can grow and reproduce only on living cells of wild or domesticated barley (Hordeum sp.). Domestication and deployment of resistant barley cultivars by humans selected for amplification of Bgh isolates with different virulence combinations. We sequenced the genomes of two European Bgh isolates, A6 and K1, for comparative analysis with the reference genome of isolate DH14. This revealed a mosaic genome structure consisting of large isolate-specific DNA blocks with either high or low SNP densities. Some of the highly polymorphic blocks likely accumulated SNPs for over 10,000 years, well before the domestication of barley. These isolate-specific blocks of alternating monomorphic and polymorphic regions imply an exceptionally large standing genetic variation in the Bgh population and might be generated and maintained by rare outbreeding and frequent clonal reproduction. RNA-sequencing experiments with isolates A6 and K1 during four early stages of compatible and incompatible interactions on leaves of partially immunocompromised Arabidopsis mutants revealed a conserved Bgh transcriptional program during pathogenesis compared with the natural host barley despite ~200 million years of reproductive isolation of these hosts. Transcripts encoding candidate-secreted effector proteins are massively induced in successive waves. A specific decrease in candidate-secreted effector protein transcript abundance in the incompatible interaction follows extensive transcriptional reprogramming of the host transcriptome and coincides with the onset of localized host cell death, suggesting a host-inducible defense mechanism that targets fungal effector secretion or production.
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Affiliation(s)
| | | | - Takaki Maekawa
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Saskia Vernaldi
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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87
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Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G. Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1575-1586. [PMID: 23494394 DOI: 10.1007/s00122-013-2075-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/23/2013] [Indexed: 06/01/2023]
Abstract
The barley Rdg2a locus confers resistance to the leaf stripe pathogen Pyrenophora graminea and, in the barley genotype Thibaut, it is composed of a gene family with three highly similar paralogs. Only one member of the gene family (called as Rdg2a) encoding for a CC-NB-LRR protein is able to confer resistance to the leaf stripe isolate Dg2. To study the genome evolution and diversity at the Rdg2a locus, sequences spanning the Rdg2a gene were compared in two barley cultivars, Thibaut and Morex, respectively, resistant and susceptible to leaf stripe. An overall high level of sequence conservation interrupted by several rearrangements that included three main deletions was observed in the Morex contig. The main deletion of 13,692 bp was most likely derived from unequal crossing over between Rdg2a paralogs leading to the generation of a chimeric Morex rdg2a gene which was not associated to detectable level of resistance toward leaf stripe. PCR-based analyses of genic and intergenic regions at the Rdg2a locus in 29 H. vulgare lines and one H. vulgare ssp. spontaneum accession indicated large haplotype variability in the cultivated barley gene pool suggesting rapid and recent divergence at this locus. Barley genotypes showing the same haplotype as Thibaut at the Rdg2a locus were selected for a Rdg2a allele mining through allele re-sequencing and two lines with polymorphic nucleotides leading to amino acid changes in the CC-NB and LRR encoding domains, respectively, were identified. Analysis of nucleotide diversity of the Rdg2a alleles revealed that the polymorphic sites were subjected to positive selection. Moreover, strong positively selected sites were located in the LRR encoding domain suggesting that both positive selection and divergence at homologous loci are possibly representing the molecular mechanism for the generation of high diversity at the Rdg2a locus in the barley gene pool.
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Affiliation(s)
- Chiara Biselli
- Genomics Research Centre, CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Via S Protaso 302, 29017 Fiorenzuola d'Arda, Piacenza, Italy
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88
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Chang C, Yu D, Jiao J, Jing S, Schulze-Lefert P, Shen QH. Barley MLA immune receptors directly interfere with antagonistically acting transcription factors to initiate disease resistance signaling. THE PLANT CELL 2013; 25:1158-73. [PMID: 23532068 PMCID: PMC3634683 DOI: 10.1105/tpc.113.109942] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
The nucleotide binding domain and Leucine-rich repeat (NLR)-containing proteins in plants and animals mediate pathogen sensing inside host cells and mount innate immune responses against microbial pathogens. The barley (Hordeum vulgare) mildew A (MLA) locus encodes coiled-coil (CC)-type NLRs mediating disease resistance against the powdery mildew pathogen Blumeria graminis. Here, we report direct interactions between MLA and two antagonistically acting transcription factors, MYB6 and WRKY1. The N-terminal CC signaling domain of MLA interacts with MYB6 to stimulate its DNA binding activity. MYB6 functions as a positive regulator of basal and MLA-mediated immunity responses to B. graminis. MYB6 DNA binding is antagonized by direct association with WRKY1 repressor, which in turn also interacts with the MLA CC domain. The activated form of full-length MLA10 receptor is needed to release MYB6 activator from WRKY1 repression and to stimulate MYB6-dependent gene expression. This implies that, while sequestered by the WRKY1 repressor in the presence of the resting immune receptor, MYB6 acts as an immediate and positive postactivation signaling component of the active state of MLA during transcriptional reprogramming for innate immune responses.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deshui Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Jiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaojuan Jing
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Address correspondence to
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89
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Ngo QA, Albrecht H, Tsuchimatsu T, Grossniklaus U. The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity. BMC PLANT BIOLOGY 2013; 13:28. [PMID: 23419068 PMCID: PMC3599707 DOI: 10.1186/1471-2229-13-28] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/11/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plant parasitism represents an extraordinary interaction among flowering plants: parasitic plants use a specialized organ, the haustorium, to invade the host vascular system to deprive host plants of water and nutrients. Various compounds present in exudates of host plants trigger haustorium development. The two most effective haustorium inducing factors (HIFs) known for the parasitic plant Triphysaria versicolor (T. versicolor) are peonidin, an antioxidant flavonoid, and 2,6-dimethoxybenzoquinone (DMBQ), an oxidative stress agent. To date, two genes involved in haustorium initiation in T. versicolor have been identified: TvQR1, a quinone oxidoreductase that generates the active HIF from DMBQ, and TvPirin, a transcription co-factor that regulates several other DMBQ- responsive and -non-responsive genes. While the expression of these genes in response to DMBQ is well characterized, their expression in response to peonidin is not. In addition, the pattern of polymorphisms in these genes is unknown, even though nucleotide changes in TvQR1 and TvPirin may have contributed to the ability of T. versicolor to develop haustoria. To gain insights into these aspects, we investigated their transcriptional responses to HIFs and non-HIF and their natural nucleotide diversity. RESULTS Here we show that TvQR1 and TvPirin are transcriptionally upregulated by both DMBQ and peonidin in T. versicolor roots. Yet, while TvQR1 also responded to juglone, a non-HIF quinone with toxicity comparable to that of DMBQ, TvPirin did not. We further demonstrate that TvPirin encodes a protein shorter than the one previously reported. In the T. versicolor natural population of Northern California, TvQR1 exhibited remarkably higher molecular diversity and more recombination events than TvPirin, with the highest non-synonymous substitution rate in the substrate recognition and catalytic domain of the TvQR1 protein. CONCLUSION Our results suggest that TvQR1 and TvPirin have most likely evolved highly distinct roles for haustorium formation. Unlike TvPirin, TvQR1 might have been under diversifying selection to maintain a diverse collection of polymorphisms, which might be related to the recognition of an assortment of HIF and non-HIF quinones as substrates for successful haustorial establishment in a wide range of host plants.
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Affiliation(s)
- Quy A Ngo
- Genetics Graduate Group, University of California – Davis, One Shields Avenue, Davis, CA 95616, USA
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Huguette Albrecht
- Department of Public Health Sciences, School of Medicine, University of California – Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Ueli Grossniklaus
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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90
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Blümke A, Somerville SC, Voigt CA. Transient expression of the <i>Arabidopsis thaliana</i> callose synthase PMR4 increases penetration resistance to powdery mildew in barley. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.48106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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91
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Abstract
The nucleotide-binding domain and leucine-rich repeat (NLR) family of plant receptors detects pathogen-derived molecules, designated effectors, inside host cells and mediates innate immune responses to pathogenic invaders. Genetic evidence revealed species-specific coevolution of many NLRs with effectors from host-adapted pathogens, suggesting that the specificity of these NLRs is restricted to the host or closely related plant species. However, we report that an NLR immune receptor (MLA1) from monocotyledonous barley is fully functional in partially immunocompromised dicotyledonous Arabidopsis thaliana against the barley powdery mildew fungus, Blumeria graminis f. sp. hordei. This implies ~200 million years of evolutionary conservation of the underlying immune mechanism. A time-course RNA-seq analysis in transgenic Arabidopsis lines detected sustained expression of a large MLA1-dependent gene cluster. This cluster is greatly enriched in genes known to respond to the fungal cell wall-derived microbe-associated molecular pattern chitin. The MLA1-dependent sustained transcript accumulation could define a conserved function of the nuclear pool of MLA1 detected in barley and Arabidopsis. We also found that MLA1-triggered immunity was fully retained in mutant plants that are simultaneously depleted of ethylene, jasmonic acid, and salicylic acid signaling. This points to the existence of an evolutionarily conserved and phytohormone-independent MLA1-mediated resistance mechanism. This also suggests a conserved mechanism for internalization of B. graminis f. sp. hordei effectors into host cells of flowering plants. Furthermore, the deduced connectivity of the NLR to multiple branches of immune signaling pathways likely confers increased robustness against pathogen effector-mediated interception of host immune signaling and could have contributed to the evolutionary preservation of the immune mechanism.
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92
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A physical, genetic and functional sequence assembly of the barley genome. Nature 2012; 491:711-6. [PMID: 23075845 DOI: 10.1038/nature11543] [Citation(s) in RCA: 936] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/30/2012] [Indexed: 12/13/2022]
Abstract
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
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93
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Takken FLW, Goverse A. How to build a pathogen detector: structural basis of NB-LRR function. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:375-84. [PMID: 22658703 DOI: 10.1016/j.pbi.2012.05.001] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 05/20/2023]
Abstract
Many plant disease resistance (R) proteins belong to the family of nucleotide-binding-leucine rich repeat (NB-LRR) proteins. NB-LRRs mediate recognition of pathogen-derived effector molecules and subsequently activate host defence. Their multi-domain structure allows these pathogen detectors to simultaneously act as sensor, switch and response factor. Structure-function analyses and the recent elucidation of the 3D structures of subdomains have provided new insight in how these different functions are combined and what the contribution is of the individual subdomains. Besides interdomain contacts, interactions with chaperones, the proteasome and effector baits are required to keep NB-LRRs in a signalling-competent, yet auto-inhibited state. In this review we explore operational models of NB-LRR functioning based on recent advances in understanding their structure.
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Affiliation(s)
- Frank L W Takken
- University of Amsterdam, SILS, Molecular Plant Pathology, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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94
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Law YS, Gudimella R, Song BK, Ratnam W, Harikrishna JA. Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1. Int J Mol Sci 2012; 13:9343-9362. [PMID: 22942769 PMCID: PMC3430300 DOI: 10.3390/ijms13079343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/06/2012] [Accepted: 07/06/2012] [Indexed: 11/16/2022] Open
Abstract
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression.
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Affiliation(s)
- Yee-Song Law
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
| | - Ranganath Gudimella
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
| | - Beng-Kah Song
- School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, Selangor 46150, Malaysia; E-Mail:
| | - Wickneswari Ratnam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia; E-Mail:
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
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95
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Bai S, Liu J, Chang C, Zhang L, Maekawa T, Wang Q, Xiao W, Liu Y, Chai J, Takken FLW, Schulze-Lefert P, Shen QH. Structure-function analysis of barley NLR immune receptor MLA10 reveals its cell compartment specific activity in cell death and disease resistance. PLoS Pathog 2012; 8:e1002752. [PMID: 22685408 PMCID: PMC3369952 DOI: 10.1371/journal.ppat.1002752] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 04/30/2012] [Indexed: 11/18/2022] Open
Abstract
Plant intracellular immune receptors comprise a large number of multi-domain proteins resembling animal NOD-like receptors (NLRs). Plant NLRs typically recognize isolate-specific pathogen-derived effectors, encoded by avirulence (AVR) genes, and trigger defense responses often associated with localized host cell death. The barley MLA gene is polymorphic in nature and encodes NLRs of the coiled-coil (CC)-NB-LRR type that each detects a cognate isolate-specific effector of the barley powdery mildew fungus. We report the systematic analyses of MLA10 activity in disease resistance and cell death signaling in barley and Nicotiana benthamiana. MLA10 CC domain-triggered cell death is regulated by highly conserved motifs in the CC and the NB-ARC domains and by the C-terminal LRR of the receptor. Enforced MLA10 subcellular localization, by tagging with a nuclear localization sequence (NLS) or a nuclear export sequence (NES), shows that MLA10 activity in cell death signaling is suppressed in the nucleus but enhanced in the cytoplasm. By contrast, nuclear localized MLA10 is sufficient to mediate disease resistance against powdery mildew fungus. MLA10 retention in the cytoplasm was achieved through attachment of a glucocorticoid receptor hormone-binding domain (GR), by which we reinforced the role of cytoplasmic MLA10 in cell death signaling. Together with our data showing an essential and sufficient nuclear MLA10 activity in disease resistance, this suggests a bifurcation of MLA10-triggered cell death and disease resistance signaling in a compartment-dependent manner.
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Affiliation(s)
- Shiwei Bai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ling Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Takaki Maekawa
- Department of Plant Microbe Interactions, Max-Planck Institut Pflanzenzüchtungsforschung, Cologne, Germany
| | - Qiuyun Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenkai Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yule Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jijie Chai
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Frank L. W. Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Centre for BioSystem Genomics, Wageningen, The Netherlands
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max-Planck Institut Pflanzenzüchtungsforschung, Cologne, Germany
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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96
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Moeller JR, Moscou MJ, Bancroft T, Skadsen RW, Wise RP, Whitham SA. Differential accumulation of host mRNAs on polyribosomes during obligate pathogen-plant interactions. MOLECULAR BIOSYSTEMS 2012; 8:2153-65. [PMID: 22660698 DOI: 10.1039/c2mb25014d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Plant pathogens elicit dramatic changes in the expression of host genes during both compatible and incompatible interactions. Gene expression profiling studies of plant-pathogen interactions have only considered messenger RNAs (mRNAs) present in total RNA, which contains subpopulations of actively translated mRNAs associated with polyribosomes (polysomes) and non-translated mRNAs that are not associated with polysomes. The goal of this study was to enhance previous gene expression analyses by identifying host mRNAs that become differentially associated with polysomes following pathogen inoculation. Total and polysomal RNA were extracted from barley (Hordeum vulgare) plants at 32 h after inoculation with Blumeria graminis f. sp. hordei, and Arabidopsis thaliana plants at 10 days after inoculation with Turnip mosaic virus. Gene expression profiles were obtained for each pathosystem, which represent diverse plant host-obligate pathogen interactions. Using this approach, host mRNAs were identified that were differentially associated with polysomes in response to pathogen treatment. Approximately 18% and 26% of mRNAs represented by probe sets on the Affymetrix Barley1 and Arabidopsis ATH1 GeneChips, respectively, differentially accumulated in the two populations in one or more combinations of treatment and genotype. Gene ontology analysis of mRNAs sharing the same pattern of accumulation in total and polysomal RNA identified gene sets that contained a significant number of functionally related annotations, suggesting both transcript accumulation and recruitment to polyribosomes are coordinately regulated in these systems.
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Affiliation(s)
- Jackson R Moeller
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, USA
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97
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Rayapuram C, Jensen MK, Maiser F, Shanir JV, Hornshøj H, Rung JH, Gregersen PL, Schweizer P, Collinge DB, Lyngkjær MF. Regulation of basal resistance by a powdery mildew-induced cysteine-rich receptor-like protein kinase in barley. MOLECULAR PLANT PATHOLOGY 2012; 13:135-47. [PMID: 21819533 PMCID: PMC6638725 DOI: 10.1111/j.1364-3703.2011.00736.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The receptor-like protein kinases (RLKs) constitute a large and diverse group of proteins controlling numerous plant physiological processes, including development, hormone perception and stress responses. The cysteine-rich RLKs (CRKs) represent a prominent subfamily of transmembrane-anchored RLKs. We have identified a putative barley (Hordeum vulgare) CRK gene family member, designated HvCRK1. The mature putative protein comprises 645 amino acids, and includes a putative receptor domain containing two characteristic 'domain 26 of unknown function' (duf26) domains in the N-terminal region, followed by a rather short 17-amino-acid transmembrane domain, which includes an AAA motif, two features characteristic of endoplasmic reticulum (ER)-targeted proteins and, finally, a characteristic putative protein kinase domain in the C-terminus. The HvCRK1 transcript was isolated from leaves inoculated with the biotrophic fungal pathogen Blumeria graminis f.sp. hordei (Bgh). HvCRK1 transcripts were observed to accumulate transiently following Bgh inoculation of susceptible barley. Transient silencing of HvCRK1 expression in bombarded epidermal cells led to enhanced resistance to Bgh, but did not affect R-gene-mediated resistance. Silencing of HvCRK1 phenocopied the effective penetration resistance found in mlo-resistant barley plants, and the possible link between HvCRK1 and MLO was substantiated by the fact that HvCRK1 induction on Bgh inoculation was dependent on Mlo. Finally, using both experimental and in silico approaches, we demonstrated that HvCRK1 localizes to the ER of barley cells. The negative effect on basal resistance against Bgh and the functional aspects of MLO- and ER-localized HvCRK1 signalling on Bgh inoculation are discussed.
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Affiliation(s)
- Cbgowda Rayapuram
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
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98
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Di Gaspero G, Copetti D, Coleman C, Castellarin SD, Eibach R, Kozma P, Lacombe T, Gambetta G, Zvyagin A, Cindrić P, Kovács L, Morgante M, Testolin R. Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:277-86. [PMID: 21947344 DOI: 10.1007/s00122-011-1703-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 09/07/2011] [Indexed: 05/20/2023]
Abstract
The Rpv3 locus is a major determinant of downy mildew resistance in grapevine (Vitis spp.). A selective sweep at this locus was revealed by the DNA genotyping of 580 grapevines, which include a highly diverse set of 265 European varieties that predated the spread of North American mildews, 82 accessions of wild species, and 233 registered breeding lines with North American ancestry produced in the past 150 years. Artificial hybridisation and subsequent phenotypic selection favoured a few Rpv3 haplotypes that were introgressed from wild vines and retained in released varieties. Seven conserved haplotypes in five descent groups of resistant varieties were traced back to their founders: (1) 'Munson', a cross between two of Hermann Jaeger's selections of V. rupestris and V. lincecumii made in the early 1880s in Missouri, (2) V. rupestris 'Ganzin', first utilised for breeding in 1879 by Victor Ganzin in France, (3) 'Noah', selected in 1869 from intermingled accessions of V. riparia and V. labrusca by Otto Wasserzieher in Illinois, (4) 'Bayard', a V. rupestris × V. labrusca offspring generated in 1882 by George Couderc in France, and (5) a wild form closely related to V. rupestris accessions in the Midwestern United States and introgressed into 'Seibel 4614' in the 1880s by Albert Seibel in France. Persistence of these Rpv3 haplotypes across many of the varieties generated by human intervention indicates that a handful of vines with prominent resistance have laid the foundation for modern grape breeding. A rampant hot spot of NB-LRR genes at the Rpv3 locus has provided a distinctive advantage for the adaptation of native North American grapevines to withstand downy mildew. The coexistence of multiple resistance alleles or paralogues in the same chromosomal region but in different haplotypes counteracts efforts to pyramidise them in a diploid individual via conventional breeding.
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Affiliation(s)
- Gabriele Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle scienze 208, 33100, Udine, Italy.
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Schweizer P, Stein N. Large-scale data integration reveals colocalization of gene functional groups with meta-QTL for multiple disease resistance in barley. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1492-501. [PMID: 21770767 DOI: 10.1094/mpmi-05-11-0107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Race-nonspecific and durable resistance of plant genotypes to major pathogens is highly relevant for yield stability and sustainable crop production but difficult to handle in practice due to its polygenic inheritance by quantitative trait loci (QTL). As far as the underlying genes are concerned, very little is currently known in the most important crop plants such as the cereals. Here, we integrated publicly available data for barley (Hordeum vulgare subsp. vulgare) in order to detect the most important genomic regions for QTL-mediated resistance to a number of fungal pathogens and localize specific functional groups of genes within these regions. This identified 20 meta-QTL, including eight hot spots for resistance to multiple diseases that were distributed over all chromosomes. At least one meta-QTL region for resistance to the powdery mildew fungus Blumeria graminis was found to be co-linear between barley and wheat, suggesting partial evolutionary conservation. Large-scale genetic mapping revealed that functional groups of barley genes involved in secretory processes and cell-wall reinforcement were significantly over-represented within QTL for resistance to powdery mildew. Overall, the results demonstrate added value resulting from large-scale genetic and genomic data integration and may inform genomic-selection procedures for race-nonspecific and durable disease resistance in barley.
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Affiliation(s)
- Patrick Schweizer
- Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung, Germany.
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Abstract
In plants and animals, the NLR family of receptors perceives non-self and modified-self molecules inside host cells and mediates innate immune responses to microbial pathogens. Despite their similar biological functions and protein architecture, animal NLRs are normally activated by conserved microbe- or damage-associated molecular patterns, whereas plant NLRs typically detect strain-specific pathogen effectors. Plant NLRs recognize either the effector structure or effector-mediated modifications of host proteins. The latter indirect mechanism for the perception of non-self, as well as the within-species diversification of plant NLRs, maximize the capacity to recognize non-self through the use of a finite number of innate immunoreceptors. We discuss recent insights into NLR activation, signal initiation through the homotypic association of N-terminal domains and subcellular receptor dynamics in plants and compare those with NLR functions in animals.
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