Tree Genetics & Genomes

, Volume 2, Issue 4, pp 202–224

Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

  • E. Silfverberg-Dilworth
  • C. L. Matasci
  • W. E. Van de Weg
  • M. P. W. Van Kaauwen
  • M. Walser
  • L. P. Kodde
  • V. Soglio
  • L. Gianfranceschi
  • C. E. Durel
  • F. Costa
  • T. Yamamoto
  • B. Koller
  • C. Gessler
  • A. Patocchi
Original Paper


A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database ( to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15 cM.


SSR Genetic mapping Simple sequence repeat 


  1. Benson G (1999) Tandem repeat finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580PubMedCrossRefGoogle Scholar
  2. Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by tag DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20:1004–1010PubMedGoogle Scholar
  3. Bus V, Van de Weg WE, Durel CE, Gessler C, Parisi L, Rikkerink E, Gardiner S, Meulenbroek B, Calenge F, Patocchi A, Laurens F (2004) Delineation of a scab resistance gene cluster on linkage group 2 of apple. Acta Hortic 663:57–62Google Scholar
  4. Bus VGM, Rikkerink EHA, van de Weg WE, Rusholme RL, Gardiner SE, Bassett HCM, Kodde LP, Parisi L, Laurens FND, Meulenbroek EJ, Plummer KM (2005a) The Vh2 and Vh4 scab resistance genes in two differential hosts derived from Russian apple R12740-7A map to the same linkage group of apple. Mol Breed 15:103–116CrossRefGoogle Scholar
  5. Bus VGM, Laurens FND, Van de Weg WE, Rusholme RL, Rikkerink EHA, Gardiner SE, Bassett HCM, Plummer KM (2005b) The Vh8 locus of a new gene-for-gene interaction between Venturia inaequalis and the wild apple Malus sieversii is closely linked to the Vh2 locus in Malus pumila R12740-7A. New Phytol 166:1035–1049PubMedCrossRefGoogle Scholar
  6. Calenge F, Durel CE (2005) Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments. Mol Breed (in press). DOI 10.1007/s11032-006-9004-7
  7. Calenge F, Faure A, Goerre M, Gebhardt C, Van de Weg WE, Parisi L, Durel C-E (2004) Quantitative Trait Loci (QTL) analysis reveals both broad-spectrum and isolate-specific QTL for scab resistance in an apple progeny challenged with eight isolates of Venturia inaequalis. Phytopathology 94:370–379CrossRefGoogle Scholar
  8. Calenge F, Drouet D, Denance C, Van de Weg WE, Brisset M-N, Paulin JP, Durel CE (2005) Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies. Theor Appl Genet 111:128–135PubMedCrossRefGoogle Scholar
  9. Conner JP, Brown SK, Weeden NF (1998) Molecular-marker analysis of quantitative traits for growth and development in juvenile apple trees. Theor Appl Genet 96:1027–1035CrossRefGoogle Scholar
  10. Costa F, Stella S, Van de Weg WE, Guerra W, Cecchinel M, Dallavia J, Koller B, Sansavini S (2005) Role of the genes Md-ACO1 and Md-ACS1 in ethylene production and shelf life of apple (Malus domestica Borkh). Euphytica 141:181–190CrossRefGoogle Scholar
  11. Coart E, Vekemans X, Smulders MJM, Wagner I, Van Huylenbroeck J, Van Bockstaele E, Roldán-Ruiz I (2003) Genetic variation in the endangered Wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by AFLP and microsatellite markers. Consequences for conservation. Mol Ecol 12:845–857PubMedCrossRefGoogle Scholar
  12. Crowhurst RN, Allan AC, Atkinson RG, Beuning LL, Davy M, Friel E, Gardiner SE, Gleave AP, Greenwood DR, Hellens RP, Janssen BJ, Kutty-Amma S, Laing WA, MacRae EA, Newcomb RD, Plummer KM, Schaffer R, Simpson RM, Snowden KC, Templeton MD, Walton EF, Rikkerink EHA (2005) The HortResearch apple EST database—a resource for apple genetics and functional genomics. In: Proceedings of Plant and Animal Genomes XIII Conference, Abstract P499, San Diego, CaliforniaGoogle Scholar
  13. Dondini L, Pierantoni L, Gaiotti F, Chiodini R, Tartarini S, Bazzi C, Sansavini S (2004) Identifying QTLs for fire-blight resistance via a European pear (Pyrus communis L.) genetic linkage map. Mol Breed 14:407–418CrossRefGoogle Scholar
  14. Durel CE, Van de Weg WE, Venisse JS, Parisi L (2000) Localization of a major gene for apple scab resistance on the European genetic map of the Prima × Fiesta cross. OILB/WPRS Bull 23:245–248Google Scholar
  15. Durel CE, Parisi L, Laurens F, Van de Weg WE, Liebhard R, Jourjon MF (2003) Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple. Genome 46:224–234PubMedCrossRefGoogle Scholar
  16. Durel CE, CalengeF, Parisi L, Van de Weg WE, Kodde LP, Liebhard R, Gessler C, Thiermann M, Dunemann F, Gennari F, Tartarini F, Lespinasse Y (2004) Overview on position and robustness of scab resistance QTL and major genes by alignment of genetic maps in five apple progenies. Acta Hortic 663:135–140Google Scholar
  17. Erdin N, Tartarini S, Broggini GAL, Gennari F, Sansavini S, Gessler C, Patocchi A (2006) Mapping of the apple scab-resistance gene Vb (submitted)Google Scholar
  18. Evans KM, James CM (2003) Identification of SCAR markers linked to Pl-w mildew resistance in apple. Theor Appl Genet 106:1178–1183PubMedGoogle Scholar
  19. Gao ZH, Van de Weg WE (2006) The Vf gene for scab resistance in apple is linked to sub-lethal genes. Euphytica (submitted)Google Scholar
  20. Gao ZS, van de Weg WE, Schaart JG, Schouten HJ, Tran DH, Kodde LP, van der Meer IM, van der Geest AHM, Kodde J, Breiteneder H, Hoffmann-Sommergruber H, Bosch D, Gilissen LJWJ (2005a) Genomic cloning and linkage mapping of the Mal d 1 (PR-10) gene family in apple (Malus domestica). Theor Appl Genet 111:171–183PubMedCrossRefGoogle Scholar
  21. Gao ZS, Van de Weg WE, Schaart JG, Van Arkel G, Breiteneder H, Hoffmann-Sommergruber H, Gilissen LJWJ (2005b) Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin). Theor Appl Genet 111:1087–1097PubMedCrossRefGoogle Scholar
  22. Gardiner SE, Bus V, Chagne D, Ranatunga C, Legg W, Bassett H, Zhou J, Cook M, Crowhurst R, Gleave A, Rikkerink E, Patocchi A, Durel C-E (2006) Mapping of major resistances to woolly apple aphid. In: Proceedings of the Plant and Animal Genomes XIV Conference, P495 (Abstract), San Diego, CaliforniaGoogle Scholar
  23. Gautschi B, Tenzer I, Muller JP, Schmid B (2000) Isolation and characterization of microsatellite loci in the bearded vulture (Gypaetus barbatus) and cross-amplification in three Old World vulture species. Mol Ecol 9:2193–2195PubMedCrossRefGoogle Scholar
  24. Gianfranceschi L, Soglio V (2004) The European project HiDRAS: innovative multidisciplinary approaches to breeding high quality disease resistant apples. Acta Hort 663:327–330Google Scholar
  25. Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C (1998) Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet 96:1069–1076CrossRefGoogle Scholar
  26. Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R (1997) Microsatellites in Malus X domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94:249–254CrossRefGoogle Scholar
  27. Gygax M, Gianfranceschi L, Liebhard R, Kellerhals M, Gessler C, Patocchi A (2004) Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii. Theor Appl Genet 109:1702–1709PubMedCrossRefGoogle Scholar
  28. Hemmat M, Weeden NF, Brown SK (2003) Mapping and evaluation of Malus x domestica microsatellites in apple and pear. J Am Soc Hortic Sci 128:515–520Google Scholar
  29. Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus domestica Borkh. core subset collection. Theor Appl Genet 97:671–683CrossRefGoogle Scholar
  30. Hokanson SC, Lamboy WF, Szewc-McFadden AK, McFerson JR (2001) Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids. Euphytica 118:281–294CrossRefGoogle Scholar
  31. James CM, Clarke JB, Evans KM (2004) Identification of molecular markers linked to the mildew resistance gene Pl-d in apple. Theor Appl Genet 110:175–181PubMedCrossRefGoogle Scholar
  32. Karagyozov L, Kalcheva ID, Chapman M (1993) Construction of random small-insert genomic libraries highly enriched for simple sequence repeats. Nucleic Acids Res 21:3911–3912PubMedCrossRefGoogle Scholar
  33. Kenis K, Keulemans J (2005) Genetic linkage maps of two apple cultivars (Malus × domestica Borkh.) based on AFLP and microsatellite markers. Mol Breed 15:205–219CrossRefGoogle Scholar
  34. Khan MA, Duffy B, Gessler C, Patocchi A (2006) QTL mapping of fire blight resistance in apple. Mol Breed 17:299–306CrossRefGoogle Scholar
  35. King GJ, Maliepaard C, Lynn JR, Alston FH, Durel CE, Evans KM, Griffon B, Laurens F, Manganaris AG, Schrevens E, Tartarini S, and Verhaegh J (2000) Quantitative genetic analysis and comparison of physical and sensory descriptors relating to fruit flesh firmness in apple (Malus pumila Mill.). Theor Appl Genet 100:1074–1084CrossRefGoogle Scholar
  36. Koller B, Tenzer I, Gessler C (2000) SSR analysis of apple scab lesions. Integrated control of pome fruit diseases. IOBC/WPRS Bulletin 23:93–98Google Scholar
  37. Korban SS, Vodkin LO, Liu L, Aldwinckle HS, Ksenija G, Gonzales DO, Malnoy M, Thimmapuram J, Carroll NJ, Goldsbrough P, Orvis K, Clifton S, Pape D, Martin M, Meyer R (2005) Large-scale analysis of EST sequences in the apple genome. In: Proceedings of the Plant and Animal Genomes XIII Conference, W130 (Abstract), San Diego, CaliforniaGoogle Scholar
  38. 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 x domestica Borkh.). Mol Breed 10:217–241CrossRefGoogle Scholar
  39. Liebhard R, Kellerhals M, Pfammatter W, Jermini M, Gessler C (2003a) Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Mol Biol 52:511–526PubMedCrossRefGoogle Scholar
  40. Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003b) Creating a saturated reference map for the apple (Malus x domestica Borkh.) genome. Theor Appl Genet 106:1497–1508PubMedGoogle Scholar
  41. Liebhard R, Koller B, Patocchi A, Kellerhals M, Pfammatter W, Jermini M, Gessler C (2003c) Mapping quantitative field resistance against apple scab in a “Fiesta” × “Discovery” progeny. Phytopatology 93:493–501CrossRefGoogle Scholar
  42. Maliepaard C, Jansen J, Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet Res 70:237–250CrossRefGoogle Scholar
  43. 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, den Nijs APM, Periam N, Rikkerink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, 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
  44. Oddou-Muratorio S, Aligon C, Decroocq S, Plomion C, Lamant T, Mush-Demesure B (2001) Microsatellite primers for Sorbus torminalis and related species. Mol Ecol Notes 1:297–299CrossRefGoogle Scholar
  45. Patocchi A, Gessler C (2003) Genome scanning approach (GSA), a fast method for finding molecular markers associated to any trait. In: Proceedings of the plant and animal genomes XI conference (Abstract ) San Diego, California, p 187Google Scholar
  46. Patocchi A, Bigler B, Koller B, Kellerhals M, Gessler C (2004) Vr 2: a new apple scab resistance gene. Theor Appl Genet 109:1087–1092PubMedCrossRefGoogle Scholar
  47. Patocchi A, Walser M, Tartarini S, Broggini GAL, Gennari F, Sansavini S, Gessler C (2005) Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm. Genome 48:630–636PubMedCrossRefGoogle Scholar
  48. 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
  49. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New YorkGoogle Scholar
  50. Stam P, Van Ooijen JW (1995) JoinMap™ version 2.0: software for the calculation of genetic linkage maps. CPRO-DLO, WageningenGoogle Scholar
  51. Tartarini S, Gennari F, Pratesi D, Palazzetti C, Sansavini S, Parisi L, Fouillet A, Fouillet V, Durel CE (2004) Characterisation and genetic mapping of a major scab resistance gene from the old Italian aple cultivar ‘Durello di Forlì’. Acta Hortic 663:129–133Google Scholar
  52. Tenzer I, degli Ivanissevich S, Morgante M, Gessler C (1999) Identification of microsatellite markers and their application to population genetics of Venturia inaequalis. Phytopatology 89:748–753CrossRefGoogle Scholar
  53. This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini l, Crespan M, Dangl GS, Eisenheld C, Ferreira-Monteiro F, Grando S, Ibáñez J, Lacombe T, Laucou V, Magalhães R, Meredith CP, Milani N, Peterlunger E, Regner F, Zulini L, Maul E (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458PubMedCrossRefGoogle Scholar
  54. Van de Weg WE, Voorrips RE, Finkers R, Kodde LP, Jansen J, Bink MCAM (2004) Pedigree genotyping a new pedigree-based approach of QTL identification and allele mining. Acta Hortic 663:45–50Google Scholar
  55. Van de Wiel C, Arens P, Vosman B (1999) Microsatellite retrieval in lettuce (Lactuca sativa L.). Genome 42:139–149PubMedCrossRefGoogle Scholar
  56. Van der Schoot J, Pospízková M, Vosman B, Smulders MJM (2000) Development and characterisation of microsatellite markers in black poplar (Populus nigra L.). Theor Appl Genet 101:317–322CrossRefGoogle Scholar
  57. Vinatzer BA, Patocchi A, Tartarini S, Gianfranceschi L, Sansavini S, Gessler C (2004) Isolation of two microsatellite markers from BAC clones of the Vf scab resistance region and molecular characterization of scab-resistant accessions in Malus germplasm. Plant Breed 123:321–326CrossRefGoogle Scholar
  58. Voorrips RE (2001) MapChart version 2.0: windows software for the graphical presentation of linkage maps and QTLs. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  59. Weber JL (1990) Informativeness of human (dC-dA)n polymorphisms. Genomics 7:524–530PubMedCrossRefGoogle Scholar
  60. Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002a) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecology notes 2:14–16CrossRefGoogle Scholar
  61. Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, Kotobuki K, Hayashi T, Matsuta N (2002b) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106:9–18PubMedGoogle Scholar
  62. Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002c) Simple sequence repeats for genetic analysis in pear. Euphytica 124:129–137CrossRefGoogle Scholar
  63. Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, Van de Weg WE, Hayashi T (2004) Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Hortic 663:51–56Google Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • E. Silfverberg-Dilworth
    • 1
  • C. L. Matasci
    • 1
  • W. E. Van de Weg
    • 2
  • M. P. W. Van Kaauwen
    • 2
  • M. Walser
    • 1
  • L. P. Kodde
    • 2
  • V. Soglio
    • 3
  • L. Gianfranceschi
    • 3
  • C. E. Durel
    • 4
  • F. Costa
    • 5
  • T. Yamamoto
    • 6
  • B. Koller
    • 7
  • C. Gessler
    • 1
  • A. Patocchi
    • 1
    • 8
  1. 1.Plant PathologyInstitute of Integrative Biology (IBZ), ETH ZurichZurichSwitzerland
  2. 2.Department of Biodiversity and BreedingPlant Research InternationalWageningenThe Netherlands
  3. 3.Department of Biomolecular Sciences and BiotechnologyUniversity of MilanMilanItaly
  4. 4.Genetics and Horticulture (GenHort)National Institute for Agronomical Research (INRA)BeaucouzéFrance
  5. 5.Department of Fruit Tree and Woody Plant SciencesUniversity of BolognaBolognaItaly
  6. 6.National Institute of Fruit Tree ScienceTsukubaJapan
  7. 7.Ecogenics GmbHZurich-SchlierenSwitzerland
  8. 8.LFW C16ZürichSwitzerland

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