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A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR

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Abstract

Fire blight is the most important bacterial disease in apple (Malus ×  domestica) and pear (Pyrus communis) production. Today, the causal bacterium Erwinia amylovora is present in many apple- and pear-growing areas. We investigated the natural resistance of the wild apple Malus ×  robusta 5 against E. amylovora, previously mapped to linkage group 3. With a fine-mapping approach on a population of 2,133 individuals followed by phenotyping of the recombinants from the region of interest, we developed flanking markers useful for marker-assisted selection. Open reading frames were predicted on the sequence of a BAC spanning the resistance locus. One open reading frame coded for a protein belonging to the NBS–LRR family. The in silico investigation of the structure of the candidate resistance gene against fire blight of M. ×  robusta 5, FB_MR5, led us hypothesize the presence of a coiled-coil region followed by an NBS and an LRR-like structure with the consensus ‘LxxLx[IL]xxCxxLxxL’. The function of FB_MR5 was predicted in agreement with the decoy/guard model, that FB_MR5 monitors the transcribed RIN4_MR5, a homolog of RIN4 of Arabidopsis thaliana that could interact with the previously described effector AvrRpt2EA of E. amylovora.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201

    Article  PubMed  CAS  Google Scholar 

  • Bai J, Pennill LA, Ning J, Lee SW, Ramalingam J, Webb CA, Zhao B, Sun Q, Nelson JC, Leach JE, Hulbert SH (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res 12:1871–1884

    Article  PubMed  CAS  Google Scholar 

  • Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36

    PubMed  CAS  Google Scholar 

  • Baldi P, Patocchi A, Zini E, Toller C, Velasco R, Komjanc M (2004) Cloning and linkage mapping of resistance gene homologues in apple. Theor Appl Genet 109:231–239

    Article  PubMed  CAS  Google Scholar 

  • Barakat A, Han DT, Benslimane A-A, Rode A, Bernardi G (1999) The gene distribution in the genomes of pea, tomato and date palm. FEBS Lett 463:139–142

    Article  PubMed  CAS  Google Scholar 

  • Bernardi G (2004) The organization of plant genomes. In: Bernardi G (ed) New comprehensive biochemistry. Elsevier, Amsterdam, pp 227–240

    Google Scholar 

  • Block A, Alfano JR (2011) Plant targets for Pseudomonas syringae type III effectors: virulence targets or guarded decoys? Curr Opin Microbiol 14:39–46

    Article  PubMed  CAS  Google Scholar 

  • Broggini GAL, Le Cam B, Parisi L, Wu C, Zhang HB, Gessler C, Patocchi A (2007) Construction of a contig of BAC clones spanning the region of the apple scab avirulence gene AvrVg. Fungal Genet Biol 44:44–51

    Article  PubMed  CAS  Google Scholar 

  • Broggini GAL, Galli P, Parravicini G, Gianfranceschi L, Gessler C, Patocchi A (2009) HcrVf paralogs are present on linkage groups 1 and 6 of Malus. Genome 52:129–138

    Article  PubMed  CAS  Google Scholar 

  • Calenge F, Van der Linden CG, Van de Weg E, Schouten HJ, Van Arkel G, Denance C, Durel CE (2005) Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple. Theor Appl Genet 110:660–668

    Article  PubMed  CAS  Google Scholar 

  • Caplan J, Padmanabhan M, Dinesh-Kumar SP (2008) Plant NB-LRR immune receptors: from recognition to transcriptional reprogramming. Cell Host Microbe 3:126–135

    Article  PubMed  CAS  Google Scholar 

  • Chagne D, Carlisle C, Blond C, Volz R, Whitworth C, Oraguzie N, Crowhurst R, Allan A, Espley R, Hellens R, Gardiner S (2007) Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 8:212

    Article  PubMed  Google Scholar 

  • DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249

    Article  PubMed  CAS  Google Scholar 

  • Durel CE, Denance C, Brisset MN (2009) Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes ‘Evereste’ and Malus floribunda clone 821. Genome 52:139–147

    Article  PubMed  CAS  Google Scholar 

  • FAO (2009) Food and agricultural organization of the United Nations Statistical database. FAO, Rome

    Google Scholar 

  • Flor H (1971) Current status of gene-for-gene concept. Annu Rev Phytopathol 9:275

    Article  Google Scholar 

  • Frey JE, Frey B, Sauer C, Kellerhals M (2004) Efficient low-cost DNA extraction and multiplex fluorescent PCR method for marker-assisted selection in breeding. Plant Breed 123:554–557

    Article  CAS  Google Scholar 

  • Galli P, Patocchi A, Broggini GAL, Gessler C (2010) The Rvi15 (Vr2) apple scab resistance locus contains three TIR-NBS-LRR genes. Mol Plant Microbe Interact 23:608–617

    Article  PubMed  CAS  Google Scholar 

  • Gardiner S, Norelli J, de Silva N, Fazio G, Peil A, Malnoy M, Horner M, Bowatte D, Carlisle C, Wiedow C, Wan Y, Bassett C, Baldo A, Celton J-M, Richter K, Aldwinckle H, Bus V (2012) Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions. BMC Genet 13:25

    Article  PubMed  CAS  Google Scholar 

  • Gessler C (2011) Cisgenic disease resistant apples: a product with benefits for the environment, producer and consumer. Outlooks Pest Manag 22:216–219

    Article  Google Scholar 

  • Grant M, Godiard L, Straube E, Ashfield T, Lewald J, Sattler A, Innes R, Dangl J (1995) Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269:843–846

    Article  PubMed  CAS  Google Scholar 

  • Hammond-Kosack KE, Jones JD (1997) Plant disease resistance genes. Annu Rev Plant Physiol Plant Mol Biol 48:575–607

    Article  PubMed  CAS  Google Scholar 

  • Jones DA, Jones JDG (1997) The role of leucine-rich repeat proteins in plant defences. Adv Bot Res 24:89–167

    Article  Google Scholar 

  • Juniper BE, Mabberley DJ (2006) The story of the apple. Timber Press, Portland

    Google Scholar 

  • Kajava AV, Kobe B (2002) Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information. Protein Sci 11:1082–1090

    Article  PubMed  CAS  Google Scholar 

  • Kellerhals M, Székely T, Sauer C, Frey J, Patocchi A (2009) Pyramiding scab resistances in apple breeding. Erwerbs-Obstbau 51:21–28

    Article  Google Scholar 

  • Khan M, Zhao YF, Korban S (2011) Molecular mechanisms of pathogenesis and resistance to the bacterial pathogen Erwinia amylovora, causal agent of fire blight disease in Rosaceae. Plant Mol Biol Rep 30(2):247–260

    Article  Google Scholar 

  • Kobe B, Deisenhofer J (1994) The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci 19:415–421

    Article  PubMed  CAS  Google Scholar 

  • Kruijt M, De Kock MJD, De Wit PJGM (2005) Receptor-like proteins involved in plant disease resistance. Mol Plant Pathol 6:85–97

    Article  PubMed  CAS  Google Scholar 

  • Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132

    Article  PubMed  CAS  Google Scholar 

  • Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van De Weg E, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10:217–241

    Article  CAS  Google Scholar 

  • Lupas A (1996) Prediction and analysis of coiled-coil structures. In: Russell FD (ed) Methods Enzymol. Academic, Waltham, pp 513–525

    Google Scholar 

  • Lupas A, Van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164

    Article  CAS  Google Scholar 

  • Martin G, Brommonschenkel S, Chunwongse J, Frary A, Ganal M, Spivey R, Wu T, Earle E, Tanksley S (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436

    Article  PubMed  CAS  Google Scholar 

  • McDonald BA, Linde C (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40:349–379

    Article  PubMed  CAS  Google Scholar 

  • McManus PS, Stockwell VO, Sundin GW, Jones AL (2002) Antibiotic use in plant agriculture. Annu Rev Phytopathol 40:443–465

    Article  PubMed  CAS  Google Scholar 

  • Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR–encoding genes in Arabidopsis. Plant Cell 15:809–834

    Article  PubMed  CAS  Google Scholar 

  • Ngugi HK, Lehman B, Madden LV (2011) Multiple treatment meta-analysis of products evaluated for control of fire blight in the eastern United States. Phytopathology 101:512–522

    Article  PubMed  CAS  Google Scholar 

  • Norelli JL, Aldwinckle HS (1986) Differential susceptibility of Malus spp cultivars Robusta 5, Novole, and Ottawa 523 to Erwinia amylovora. Plant Dis 70:1017–1019

    Article  Google Scholar 

  • Norelli JL, Aldwinckle HS, Beer SV (1988) Virulence of Erwinia amylovora strains to Malus sp. Novole plants grown in vitro and in the greenhouse. Phytopathology 78:1292–1297

    Article  Google Scholar 

  • Norelli JL, Farrell RE, Bassett CL, Baldo AM, Lalli DA, Aldwinckle HS, Wisniewski ME (2009) Rapid transcriptional response of apple to fire blight disease revealed by cDNA suppression subtractive hybridization analysis. Tree Genet Genomes 5:27–40

    Article  Google Scholar 

  • Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L (2007) MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res 35:W433–W437

    Article  PubMed  Google Scholar 

  • Parravicini G (2010) Candidate genes for fire blight resistance in apple cultivar ‘Evereste’. IBZ Plant Pathology, ETH, Zurich, p 149

    Google Scholar 

  • Parravicini G, Gessler C, Denance C, Lasserre-Zuber P, Vergne E, Brisset MN, Patocchi A, Durel CE, Broggini GAL (2011) Identification of serine/threonine kinase and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in the fire blight resistance quantitative trait locus of apple cultivar ‘Evereste’. Mol Plant Pathol 12:493–505

    Article  PubMed  CAS  Google Scholar 

  • Patocchi A, Vinatzer BA, Gianfranceschi L, Tartarini S, Zhang HB, Sansavini S, Gessler C (1999) Construction of a 550 kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf. Mol Gen Genet 262:884–891

    Article  PubMed  CAS  Google Scholar 

  • Paulin JP, Lachaud G, Lespinasse Y (1993) Role of the aggressiveness of strains of Erwinia amylovora in the experimental evaluation of susceptibility of apple cultivars to fire blight. Acta Hortic (ISHS) 338:375–376

    Google Scholar 

  • Pedley KF, Martin GB (2003) Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annu Rev Phytopathol 41:215–243

    Article  PubMed  CAS  Google Scholar 

  • Peil A, Garcia-Libreros T, Richter K, Trognitz FC, Trognitz B, Hanke MV, Flachowsky H (2007) Strong evidence for a fire blight resistance gene of Malus robusta located on linkage group 3. Plant Breed 126:470–475

    Article  CAS  Google Scholar 

  • Peil A, Hanke MV, Flachowsky H, Richter K, Garcia-Libreros T, Celton JM, Gardiner S, Horner M, Bus V (2008) Confirmation of the fire blight QTL of Malus × robusta 5 on linkage group 3. Acta Hortic (ISHS) 793:297–303

    CAS  Google Scholar 

  • Peil A, Flachowsky H, Hanke M-V, Richter K, Rode J (2011) Inoculation of Malus × robusta 5 progeny with a strain breaking resistance to fire blight reveals a minor QTL on LG5. Acta Hortic (ISHS) 896:357–362

    Google Scholar 

  • Rairdan GJ, Collier SM, Sacco MA, Baldwin TT, Boettrich T, Moffett P (2008) The coiled-coil and nucleotide binding domains of the potato Rx disease resistance protein function in pathogen recognition and signaling. Plant Cell 20:739–751

    Article  PubMed  CAS  Google Scholar 

  • Richter K, Fischer C (2000) Stability of fire blight resistance in apple. Acta Hortic (ISHS) 538:267–270

    Google Scholar 

  • Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    Google Scholar 

  • Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522

    Article  PubMed  CAS  Google Scholar 

  • Sanseverino W, Roma G, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR (2010) PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res 38:D814–D821

    Article  PubMed  CAS  Google Scholar 

  • Schouten HJ, Krens FA, Jacobsen E (2006) Cisgenic plants are similar to traditionally bred plants. EMBO Rep 7:750–753

    Article  PubMed  CAS  Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  • Söding J (2005) Protein homology detection by HMM–HMM comparison. Bioinformatics 21:951–960

    Article  PubMed  Google Scholar 

  • Szankowski I, Waidmann S, Degenhardt J, Patocchi A, Paris R, Silfverberg-Dilworth E, Broggini GAL, Gessler C (2009) Highly scab-resistant transgenic apple lines achieved by introgression of HcrVf2 controlled by different native promoter lengths. Tree Genet Genomes 5:349–358

    Article  Google Scholar 

  • Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE, Staskawicz BJ (1999) Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci U S A 96:14153–14158

    Article  PubMed  CAS  Google Scholar 

  • Taylor WR (1986) The classification of amino acid conservation. J Theor Biol 119:205–218

    Article  PubMed  CAS  Google Scholar 

  • Van der Biezen EA, Jones JD (1998) Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem Sci 23:454–456

    Article  PubMed  Google Scholar 

  • Van der Hoorn RAL, Kamoun S (2008) From guard to decoy: a new model for perception of plant pathogen effectors. Plant Cell 20:2009–2017

    Article  PubMed  Google Scholar 

  • Van der Zwet T (2006) Present worldwide distribution of fire blight and closely related diseases. Acta Hortic (ISHS) 704:35–36

    Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Van Ooijen G, Mayr G, Kasiem MMA, Albrecht M, Cornelissen BJC, Takken FLW (2008) Structure–function analysis of the NB-ARC domain of plant disease resistance proteins. J Exp Bot 59:1383–1397

    Article  PubMed  Google Scholar 

  • Vanblaere T, Szankowski I, Schaart J, Schouten H, Flachowsky H, Broggini GAL, Gessler C (2011) The development of a cisgenic apple plant. J Biotechnol 154:304–311

    Article  PubMed  CAS  Google Scholar 

  • Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel C-E, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839

    Article  PubMed  CAS  Google Scholar 

  • Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–951

    PubMed  CAS  Google Scholar 

  • Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z-X, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci U S A 95:1663–1668

    Article  PubMed  CAS  Google Scholar 

  • Zhao YF, He SY, Sundin GW (2006) The Erwinia amylovora avrRpt2(EA) gene contributes to virulence on pear and AvrRpt2(EA) is recognized by Arabidopsis RPS2 when expressed in Pseudomonas syringae. Mol Plant Microbe Interact 19:644–654

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We acknowledge the Genetic Diversity Center of ETH Zurich, Switzerland, for sequencing, fragment analysis and bioinformatics support, as well as LeRoux P-M and Baumgartner I from Agroscope Changins-Wädenswil (Switzerland) and Malnoy M from FEM/IASMA, Italy, for technical support. For financial funding, we thank the Federal Office for Agriculture FOAG of Switzerland (project: ZUEFOS) as well as the D-A-CH (German–Austrian–Swiss project: 310030L_130811).

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Authors and Affiliations

  1. Plant Pathology Integrative Biology Zurich (IBZ), Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland

    Johannes Fahrentrapp, Giovanni A. L. Broggini & Cesare Gessler

  2. Agroscope Changins-Wädenswil (ACW), Wädenswil, Switzerland

    Markus Kellerhals

  3. Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticulture and Fruit Crops, Dresden, Germany

    Andreas Peil

  4. Julius Kühn-Institut, Federal Research Center for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany

    Klaus Richter

  5. Fondazione Edmund Mach–FEM, Istituto Agrario San Michele (IASMA), S. Michele all’Adige, TN, Italy

    Elena Zini

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  1. Johannes Fahrentrapp
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  2. Giovanni A. L. Broggini
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  3. Markus Kellerhals
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  4. Andreas Peil
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  5. Klaus Richter
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  6. Elena Zini
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  7. Cesare Gessler
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Correspondence to Cesare Gessler.

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Communicated by E. Dirlewanger

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Fahrentrapp, J., Broggini, G.A.L., Kellerhals, M. et al. A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR. Tree Genetics & Genomes 9, 237–251 (2013). https://doi.org/10.1007/s11295-012-0550-3

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