Molecular Breeding

, Volume 34, Issue 2, pp 407–419 | Cite as

Identification of a major quantitative trait locus for resistance to fire blight in the wild apple species Malus fusca

  • Ofere Emeriewen
  • Klaus Richter
  • Andrzej Kilian
  • Elena Zini
  • Magda-Viola Hanke
  • Mickael Malnoy
  • Andreas PeilEmail author


Fire blight, caused by the Gram-negative bacterium Erwinia amylovora, is the most important bacterial disease affecting apple (Malus × domestica) and pear (Pyrus communis) production. The use of antibiotic treatment, though effective to some degree, is forbidden or strictly regulated in many European countries, and hence an alternative means of control is essential. The planting of fire blight-resistant cultivars seems to be a highly feasible strategy. In this study, we explored a segregating population derived from a cross between the wild apple species Malus fusca and the M. × domestica cultivar Idared. F1 progenies used for mapping were artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 109 cfu/ml in three different years. The averages of percentage lesion length of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal–Wallis analysis was used to determine marker–phenotype association and revealed a linkage group with Diversity Arrays Technology (DArT) markers significantly linked with fire blight. After locating the positions of the DArT markers on the Golden Delicious genome, simple sequence repeat (SSR) markers were developed from chromosome 10 to replace the DArT markers and to determine the quantitative trait locus (QTL) region. Multiple QTL mapping (MQM) revealed a strong QTL (Mfu10) on linkage group 10 of M. fusca explaining about 65.6 % of the phenotypic variation. This is the first report on a fire blight resistance QTL of M. fusca.


Malus fusca Fire blight Erwiniaamylovora QTL mapping DArT markers SSR markers 



This research is funded by the Genomics and Molecular Physiology of Fruits (GMPF) programme, (Reference number 0004915/AG/gt), Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige (Trentino), Italy.

Supplementary material

11032_2014_43_MOESM1_ESM.docx (168 kb)
Genetic map of Malus fusca 1 (DOCX 167 kb)


  1. Akbari M, Wenzel P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmenseik A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420PubMedCrossRefGoogle Scholar
  2. Aldwinckle HS, Beer SV (1979) Fire blight and its control. Hort Rev 1:425–476Google Scholar
  3. Aldwinkle HS, Way RD, Livermore JL, Preczewski L, Beer SV (1976) Fire blight in the Geneva apple collection. Fruit Varieties J 30:42–55Google Scholar
  4. Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ (2012) Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genom 13:203. doi: 10.1186/1471-2164-13-203 CrossRefGoogle Scholar
  5. Bonn WG, Van der Zwet T (2000) Distribution and economic importance of fire blight. In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB Intl, Wallingford, pp 37–53Google Scholar
  6. Calenge F, Drouet D, Denance C, Van de Weg WE, Brisset MN, Paulin JP, Durel CE (2005) Identification of a major QTL together with several minor additive or espistatic QTLs for resistance to fire blight in apple in two related progenies. Theor Appl Genet 111:128–135PubMedCrossRefGoogle Scholar
  7. Conner PJ, Brown SK, Weeden NF (1997) Randomly amplified polymorphic DNA-based genetic linkage maps of three apple cultivars. J Am Soc Hort Sci 3:350–359Google Scholar
  8. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leafs. Phytochem Bull 19:11–15Google Scholar
  9. 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 52:139–147PubMedCrossRefGoogle Scholar
  10. Fahrentrapp J, Broggini GAL, Kellerhals M, Peil A, Richter K, Zini E, Gessler C (2013) A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC-NBS-LRR. Tree Genet Genomes 9:237–251CrossRefGoogle Scholar
  11. Flachowsky H, Le Roux PM, Peil A, Patocchi A, Richter K, Hanke V (2011) Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker assisted selection. New Phytol 192:364–377PubMedCrossRefGoogle Scholar
  12. Gardiner SE, Norelli JL, De Silva N, Fazio G, Peil A, Malnoy M, Horner M, Bowatte D, Carlisle C, Wiedow C, Wan Y, Bassett CL, Baldo AM, Celton JM, Ritcher K, Aldwinckle HS, Bus VGM (2012) Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5′ accessions. BMC Genet 13:25. doi: 10.1186/1471-2156-13-25 PubMedCentralPubMedCrossRefGoogle Scholar
  13. Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever J, Korban S (2011) Integration of physical and genetic maps in apples confirms whole-genome and segmental duplications in the apple genome. J Exp Bot 14:51117–51130Google Scholar
  14. Hemmat M, Weeden NF, Manganaris AG, Lawson DM (1994) Molecular marker linkage map for apple. J Hered 85:4–11PubMedGoogle Scholar
  15. Hua J (2013) Modulation of plant immunity by light, circadian rhythm and temperature. Curr Opin Plant Biol 16:1–8CrossRefGoogle Scholar
  16. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25. doi: 10.1093/nar/29.4.e25 PubMedCentralPubMedCrossRefGoogle Scholar
  17. Johnson KB, Stockwell VO (1998) Management of fire blight: a case study in microbial ecology. Annu Rev Phytopathol 36:227–248PubMedCrossRefGoogle Scholar
  18. Jones AL, Schnabel E (2000) The development of streptomycin-resistant strains of Erwinia amylovora. In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB Intl, Wallingford, pp 335–367Google Scholar
  19. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP, and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390CrossRefGoogle Scholar
  20. Khan MA, Duffy B, Gessler C, Patocchi A (2006) QTL mapping of fire blight resistance. Mol Breed 17:299–306CrossRefGoogle Scholar
  21. Khan MW, Zhao YF, Korban SS (2012) Molecular mechanisms of pathogenesis and resistance to the bacterial pathogen Erwinia amylovora, causal agent of fire blight disease in Rosaceae. Plant Mol Biol Rep 30:247–260CrossRefGoogle Scholar
  22. Khan MW, Zhao YF, Korban SS (2013) Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiol Plantarum 148:344–353. doi: 10.1111/ppl.12068 CrossRefGoogle Scholar
  23. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Craig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89. doi: 10.1007/978-1-61779-870-2_5 PubMedCrossRefGoogle Scholar
  24. Kleinhempel H, Kegler H, Ficke W, Schaefer HJ (1984) Methods of testing apples for resistance to fire blight. Acta Hort 151:261–265Google Scholar
  25. Korban SS, Ries SM, Klopmeyer MJ, Morissey JF, Hattermann DR (1988) Genotype responses of scab-resistant apple cultivar/selections to two strains of Erwinia amylovora and the inheritance of resistance to fire blight. Ann Appl Biol 113:101–105CrossRefGoogle Scholar
  26. Le Roux PMF, Khan MA, Broggini GAL, Duffy B, Gessler C, Patocchi A (2010) Mapping of quantitative trait loci for fire blight resistance in the apple cultivars ‘Florina’ and ‘Nova Easygro’. Genome 53:710–722PubMedCrossRefGoogle Scholar
  27. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg WE, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10:217–241CrossRefGoogle Scholar
  28. Lu XP, Gui YJ, Xiao BG, Li YP, Tong ZJ, Liu Y, Bai XF, Wu WR, Xia L, Huttner E, Kilian A, Fan LJ (2013) Development of DArT markers for a linkage map of flue-cured tobacco. Chin Sci Bull 58:641–648. doi: 10.1007/s11434-012-5453-z CrossRefGoogle Scholar
  29. Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Hunter E, Wenzl P, Kilian A (2008) DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genom 9:26. doi: 10.1186/1471-2229-9-13 CrossRefGoogle Scholar
  30. Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, Nijs APM, Periam N, Rikkerink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, den Verhaegh JJ, Vrielink van Ginkel M, King GJ (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73CrossRefGoogle Scholar
  31. Malnoy M, Martens S, Norelli JL, Barny M, Sundin GW, Smiths THM, Brion D (2012) Fire blight: applied genomic insights of the pathogen and host. Annu Rev Phytopathol 50:475–494PubMedCrossRefGoogle Scholar
  32. McManus PS, Stockwell VO, Sundin GW, Jones AL (2002) Antibiotic use in plant agriculture. Annu Rev Phytopathol 40:443–465PubMedCrossRefGoogle Scholar
  33. Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, Velasco R, Salvi S (2011) Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet Genomes 7:857–868CrossRefGoogle Scholar
  34. Norelli JN, Aldwinckle HS (1986) Differential susceptibility of Malus spp. cultivars Robusta 5, Novole, and Ottawa 523 to Erwinia amylovora. Plant Dis 70:1017–1019CrossRefGoogle Scholar
  35. Norelli JL, Jones AL, Aldwinkle HS (2003) Fire blight management in the twenty-first century—using new technologies that enhance host resistance in apple. Plant Dis 87:756–765CrossRefGoogle Scholar
  36. Oh C-S, Beer SV (2005) Molecular genetics of Erwinia amylovora involved in the development of fire blight. FEMS Microbiol Lett 253:185–192PubMedCrossRefGoogle Scholar
  37. 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 12:493–505PubMedCrossRefGoogle Scholar
  38. 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 126:270–475CrossRefGoogle Scholar
  39. 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 Hort 793:297–303Google Scholar
  40. Peil A, Bus VGM, Geider K, Richter K, Flachowsky H, Hanke MV (2009) Improvement of fire blight resistance in apple and pear. Int J Plant Breed 3:1–27CrossRefGoogle Scholar
  41. 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 Hort 986:357–362Google Scholar
  42. Rademacher W, Kober R (2003) Efficient use of Prohexadione-Ca in pome fruits. Eur J Hort Sci 68:101–107Google Scholar
  43. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totowa, NJ, pp 365–386Google Scholar
  44. Schouten HJ, van de Weg EW, Carling J, Khan SA, McKay SJ, van Kaauwen PW, Wittenberg AHJ, Koehorst van Putten HJJ, Noordijk Y, Gao Z, Rees DJG, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A (2012) Diversity array technology (DArT) markers in apple for genetic linkage maps. Mol Breed 29:645–660. doi: 10.1007/s11032-011-9579-5 PubMedCentralPubMedCrossRefGoogle Scholar
  45. Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Biotechnol 18:233–234PubMedCrossRefGoogle Scholar
  46. Silfverberg-Dilworth E, Matasci CL, Vande Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patacchi A (2006) Microsatellite markers spanning the apple (Malus v domestica Borkh) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
  47. Soriano JM, Joshi SG, Van Kaauwen M, Noordijk J, Groenwold R, Henken B, Van de Weg WE, Schouten HJ (2009) Identification and mapping of the novel apple scab resistance gene Vd3. Tree Genet Genomes 5:475–482CrossRefGoogle Scholar
  48. Thomson SV (2000) Epidemiology of fire blight. In: Vanneste JL (ed) Fire blight: the disease and its causative agent, Erwinia amylovora. CAB International, Wallingford, pp 9–36Google Scholar
  49. Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzel P, Rines HW, Bjornstad, Howarth CJ, Jannink JL, Anderson JM, Rossnagel BG, Stuthman DD, Sorrells ME, Jackson EW, Tuvesson S, Kolb FL, Olsson O, Federizzi LC, Carson ML, Ohm HW, Molnar SJ, Scoles GJ, Eckstein PE, Bonman JM, Ceplitis A, Langdon T (2009) New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genom 21:10–39Google Scholar
  50. Tobler A, Short S, Andersen M, Paner T, Briggs J, Lambert S, Wu P, Wang Y, Spoonde A, Koehler R, Peyret N, Chen C, Broomer A, Ridzon D, Zhou H, Hoo B, Hayashibara K, Leong L, Ma C, Rosenblum B, Day J, Ziegle J, De La Vega F, Rhodes M, Hennessy K, Wenz H (2005) The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Technol 16:398–406Google Scholar
  51. Van Ooijen JW (2004) MapQTL® 5 Software for the mapping of quantitative trait loci in experimental populations. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  52. Van Ooijen JW, Maliepaard C (1996) MapQTL 4.0. Software for the calculation of QTL positions on genetic maps. CPRO-DLO, Wageningen, The NetherlandsGoogle Scholar
  53. Van Ooijen JW, Voorrips RE (2001) JOINMAP® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  54. Vanneste JL (2000) What is fire blight? Who is Erwinia amylovora? How to control it? In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB International, Wallingford, pp 1–6Google Scholar
  55. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839PubMedCrossRefGoogle Scholar
  56. Vogt I, Wöhner T, Richter K, Flachowsky H, Sundin GW, Wensing A, Savory EA, Geider K, Day B, Hanke MV, Peil A (2013) Gene-for-gene relationship in the host-pathogen system Malus × robusta 5-Erwinia amylovora. New Phytol 197:1262–1275PubMedCrossRefGoogle Scholar
  57. Wenzel P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920CrossRefGoogle Scholar
  58. White J, Law JR, McKay I, Chalmers KJ, Smith JSC, Kilian A, Powell W (2008) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453PubMedCrossRefGoogle Scholar
  59. Wittenberg AHJ, Van der Lee T, Cayla C, Kilian A, Visser RGF, Schouten HJ (2005) Validation of the high throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Genet Genomics 274:30–39PubMedCrossRefGoogle Scholar
  60. Xia L, Peng K, Yang S, Wenzl P, de Vicente MC, Fregene M, Kilian A (2005) DArT of high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098PubMedCrossRefGoogle Scholar
  61. Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong X, Kilian A (2006) Low level of genetic diversity in cultivated pigeon pea compared to its wild relatives is revealed by diversity arrays technology (DArT). Theor Appl Genet 113:585–595PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ofere Emeriewen
    • 1
    • 2
  • Klaus Richter
    • 3
  • Andrzej Kilian
    • 4
  • Elena Zini
    • 1
  • Magda-Viola Hanke
    • 2
  • Mickael Malnoy
    • 1
  • Andreas Peil
    • 2
    Email author
  1. 1.IASMA Research and Innovation CentreFondazione Edmund MachSan Michele all’Adige, TrentoItaly
  2. 2.Federal Research Centre for Cultivated Plants, Institute for Breeding Research on FruitJulius Kühn-Institut (JKI)DresdenGermany
  3. 3.Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceJulius Kühn-Institut (JKI)QuedlinburgGermany
  4. 4.Diversity Arrays TechnologyYarralumla, CanberraAustralia

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