Molecular Breeding

, 35:45 | Cite as

Identification of SNPs linked to eight apple disease resistance loci

  • Melanie Jänsch
  • Giovanni A. L. Broggini
  • Juliane Weger
  • Vincent G. M. Bus
  • Susan E. Gardiner
  • Heather Bassett
  • Andrea PatocchiEmail author


Although genetic and genomic studies have progressed to a very advanced level in apple, the application of this acquired knowledge for marker-assisted breeding (MAB) remains limited mainly to pyramiding monogenetically inherited resistances against apple scab, powdery mildew and fire blight. Crucial contributing reasons are the uncertainty in map position of some genes and the lack of tightly linked markers suitable for high-throughput analysis (HTA) that reduces the costs of MAB. Single-nucleotide polymorphism (SNP) markers have the potential to resolve these major issues. Here we present the refined map positions of the apple scab resistance genes Rvi2, Rvi4 and Rvi11, and the systematic search for SNPs associated with apple scab (Rvi2, Rvi4, Rvi6, Rvi11, Rvi15), powdery mildew (Pl2) and fire blight (FB_E and FB_MR5) resistances. With the aid of the ‘Golden Delicious’ sequence, several SNPs linked to each of the eight resistances were identified in the genomic regions around the resistance loci previously delimited by simple sequence repeat markers. The specificity of the alleles in coupling with the resistances was determined by screening eight apple genotypes, six of them being founding clones of modern apple cultivars. These SNPs can now be used to develop SNP-based HTA assays for MAB.


Venturia inaequalis Podosphaera leucotricha Erwinia amylovora Malus × domestica Marker-Assisted Selection 



The authors thank Dr. Elena Zini for the support in the development of the Rvi11 SSR markers. This work has been (partly) funded under the EU Seventh Framework Programme by the FruitBreedomics Project No. 265582: Integrated Approach for Increasing Breeding Efficiency in Fruit Tree Crop. The views expressed in this work are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. The New Zealand component of the research was funded by the Plant and Food Research Pipfruit Core programme 1433.

Supplementary material

11032_2015_242_MOESM1_ESM.docx (37 kb)
Supplementary material 1 (DOCX 36 kb)
11032_2015_242_MOESM2_ESM.docx (18 kb)
Supplementary material 2 (DOCX 17 kb)
11032_2015_242_MOESM3_ESM.tif (262 kb)
Example of mapping of a SNP (SNP FBsnRvi2-7_Y536) associated with the resistance gene Rvi2 and verification of the level of specificity of the allele in coupling (T). The number of resistant, susceptible, and recombinants has been reduced to two for each type of progeny plant for graphical reason. TSR34T15: resistant parent; ‘Golden Delicious’: susceptible parent; ResPP: resistant progeny plant; SusPP: susceptible progeny plant; RecSusPP: susceptible recombinant progeny plant; RecResPP: resistant recombinant progeny plant; Genotypes from ‘Braeburn’ to ‘Jonathan’: founders tested to verify the specificity of the SNP allele associated with the resistance Rvi2. As ‘Cox’ Orange Pippin’ amplifies the allele in coupling with the Rvi2 resistance markers based on this SNP will not be 100% specific for this resistance gene (TIFF 261 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Melanie Jänsch
    • 1
  • Giovanni A. L. Broggini
    • 1
    • 2
  • Juliane Weger
    • 1
    • 2
  • Vincent G. M. Bus
    • 3
  • Susan E. Gardiner
    • 4
  • Heather Bassett
    • 4
  • Andrea Patocchi
    • 1
    Email author
  1. 1.AgroscopeInstitute for Plant Production Sciences, PhytopathologyWädenswilSwitzerland
  2. 2.Plant Pathology GroupSwiss Federal Institute of TechnologyZurichSwitzerland
  3. 3.The New Zealand Institute for Plant and Food Research LimitedHavelock NorthNew Zealand
  4. 4.The New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand

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