Tree Genetics & Genomes

, Volume 5, Issue 1, pp 211–223

Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome

  • A. Patocchi
  • F. Fernández-Fernández
  • K. Evans
  • D. Gobbin
  • F. Rezzonico
  • A. Boudichevskaia
  • F. Dunemann
  • M. Stankiewicz-Kosyl
  • F. Mathis-Jeanneteau
  • C. E. Durel
  • L. Gianfranceschi
  • F. Costa
  • C. Toller
  • V. Cova
  • D. Mott
  • M. Komjanc
  • E. Barbaro
  • L. Kodde
  • E. Rikkerink
  • C. Gessler
  • W. E. van de Weg
Original Paper
  • 307 Downloads

Abstract

A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects.

Keywords

SSR Multiplex PCR Genotyping Malus 

Supplementary material

11295_2008_176_MOESM1_ESM.doc (77 kb)
ESM Table S1(DOC 80 KB)
11295_2008_176_MOESM2_ESM.doc (230 kb)
ESM Table S2(DOC 230 KB)

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • A. Patocchi
    • 1
    • 11
  • F. Fernández-Fernández
    • 2
  • K. Evans
    • 2
  • D. Gobbin
    • 1
  • F. Rezzonico
    • 1
    • 11
  • A. Boudichevskaia
    • 3
  • F. Dunemann
    • 3
  • M. Stankiewicz-Kosyl
    • 4
  • F. Mathis-Jeanneteau
    • 5
  • C. E. Durel
    • 5
  • L. Gianfranceschi
    • 6
  • F. Costa
    • 7
  • C. Toller
    • 8
  • V. Cova
    • 8
  • D. Mott
    • 8
  • M. Komjanc
    • 8
  • E. Barbaro
    • 8
  • L. Kodde
    • 9
  • E. Rikkerink
    • 10
  • C. Gessler
    • 1
  • W. E. van de Weg
    • 9
  1. 1.Plant Pathology, Institute of Integrative Biology (IBZ)ETH ZurichZurichSwitzerland
  2. 2.East Malling ResearchKentUK
  3. 3.Bundesforschungsinstitut für KulturpflanzenJulius Kühn-Institut (JKI)DresdenGermany
  4. 4.Laboratory of Basic Research in Horticulture, Faculty of Horticulture and Landscape ArchitectureWarsaw Agricultural University (WAU)WarsawPoland
  5. 5.UMR1259 Genetics and Horticulture (GenHort)Institut National de la Recherche Agronomique (INRA)BeaucouzéFrance
  6. 6.Department of Biomolecular Sciences and BiotechnologyUniversity of MilanMilanItaly
  7. 7.Department of Fruit Tree and Woody Plant SciencesUniversity of BolognaBolognaItaly
  8. 8.Istituto Agrario di San Michele all’AdigeSan Michele all’AdigeItaly
  9. 9.Department of Biodiversity and BreedingPlant Research InternationalWageningenThe Netherlands
  10. 10.The Horticulture and Food Research Institute of New Zealand Ltd, Mt Albert Research CenterAucklandNew Zealand
  11. 11.Agroscope Changins-Wädenswil Research station, Plant protection, PhytopathologyWädenswilSwitzerland

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