Molecular Breeding

, 22:95 | Cite as

Linkage maps of the apple (Malus × domestica Borkh.) cvs ‘Ralls Janet’ and ‘Delicious’ include newly developed EST markers

  • Megumi Igarashi
  • Yoshie Abe
  • Yoshimichi Hatsuyama
  • Takanori Ueda
  • Tomoko Fukasawa-Akada
  • Tomoyuki Kon
  • Tsuyoshi Kudo
  • Takashi Sato
  • Masahiko Suzuki


Two apple genetic linkage maps were constructed using amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), random amplified polymorphic DNAs (RAPDs), and expressed sequence tag (EST)-derived markers in combination with a pseudo-testcross mapping strategy in which the cultivars ‘Ralls Janet’ and ‘Delicious’ were used as the respective seed parents. Mitsubakaido (Malus sieboldii) was used as the pollen parent for each of the segregating F1 populations. Expressed sequence tag data were obtained from the random sequencing of cDNA libraries constructed from in vitro cultured shoots and maturing fruits of cv ‘Fuji’, which is the offspring of a cross between ‘Ralls Janet’ and ‘Delicious’. In addition, a number of published gene sequences were used to develop markers for mapping. The ‘Ralls Janet’ map consisted of 346 markers (178 AFLPs, 95 RAPDs, 54 SSRs, 18 ESTs, and the S locus) in 17 linkage groups, with a total length of 1082 cM, while that of ‘Delicious’ comprised 300 markers (120 AFLPs, 81 RAPDs, 64 SSRs, 32 ESTs, and the S, Rf, and MdACS-1 loci) on 17 linkage groups spanning 1031 cM. These maps are amenable to comparisons with previously published maps of ‘Fiesta’ and ‘Discovery’ (Liebhard et al., Mol Breed 10:217–241, 2002; Liebhard et al., Theor Appl Genet 106:1497–1508, 2003a) because several of the SSRs (one to three markers per linkage group) were used in all of the maps. Distorted marker segregation was observed in three and two regions of the ‘Ralls Janet’ and ‘Delicious’ maps, respectively. These regions were localized in different parts of the genome from those in previously reported apple linkage maps. This marker distortion may be dependent on the combinations of cultivars used for map construction.


Apple CAPS marker Expressed sequence tag Linkage map 



We thank Dr. M. Omura for his suggestions. We also thank Ms. K. Shiratori and Ms. M. Jin for the technical assistance.


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. 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 109:231–239PubMedCrossRefGoogle Scholar
  3. Belfanti E, Silfverberg-Dilworth E, Tartarini S, Patocchi A, Barbieri M, Zhu J, Vinatzer BA, Gianfranceschi L, Gessler C, Sansavini S (2004) The HcrVf2 gene from a wild apple confers scab resistance to a transgenic cultivated variety. Proc Natl Acad Sci USA 101:886–890PubMedCrossRefGoogle Scholar
  4. Bousquet J, Simon L, Lalonde M (1990) DNA amplification from vegetative and sexual tissues of trees using polymerase chain reaction. Can J For Res 20:254–257CrossRefGoogle Scholar
  5. Broothaerts W (2003) New findings in apple S-genotype analysis resolve previous confusion and request the re-numbering of some S-alleles. Theor Appl Genet 106:703–714PubMedGoogle Scholar
  6. Broothaerts W, Janssens GA, Proost P, Broekaert F (1995) cDNA cloning and molecular analysis of two self-incompatibility alleles from apple. Plant Mol Biol 27:499–511PubMedCrossRefGoogle Scholar
  7. Calenge F, Van der Linden CG, Van de Weg E, Schouten HJ, Van Arkel G, Denancé C, Durel C-E (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 110:660–668PubMedCrossRefGoogle Scholar
  8. Cheng FS, Weeden NF, Brown SK (1996) Identification of co-dominant RAPD markers tightly linked to fruit skin color in apple. Theor Appl Genet 93:222–227CrossRefGoogle Scholar
  9. Conner PJ, Brown SK, Weeden NF (1997) Randomly amplified polymorphic DNA-based genetic linkage maps of three apple cultivars. J Am Soc Hortic Sci 122:350–359Google Scholar
  10. Conner PJ, 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
  11. Costa F, Stella S, Van de Weg WE, Guerra W, Cecchinel M, Dallavia J, Koller B, Sansavini S (2005a) 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
  12. Costa F, Stella S, Sansavini S, Van de Weg WE (2005b) Functional markers as genetic approach to study ethylene production and fruit softening in apple (Malus × domestica Borkh.). In: Mencarelli F, Tonutti P (eds) Proc 5th Int Postharvest Symp. Acta Hortic 682(ISHS):389–394Google Scholar
  13. Dirlewanger E, Graziano E, Joobeur T, Garriga-Calderé F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101:9891–9896PubMedCrossRefGoogle Scholar
  14. Gao ZS, Van de Weg WE (2006) The Vf gene for scab resistance in apple is linked to sub-lethal genes. Euphytica 151:123–132CrossRefGoogle Scholar
  15. Gao ZS, Van de Weg WE, Schaart JG, Shouten HJ, Tran DH, Kodde LP, van der Meer IM, van der Geest AHM, Kodde J, Breiteneder H, Hoffmann-Sommergruber K, 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
  16. Gao ZS, Van de Weg WE, Schaart JG, van Arkel G, Breiteneder H, Hoffmann-Sommergruber K, 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
  17. Gao ZS, Van de Weg WE, Schaart JG, van der Meer IM, Kodde L, Laimer M, Breiteneder H, Hoffmann-Sommergruber K, Gilissen LJWJ (2005c) Linkage map positions and allelic diversity of two Mal d 3 (non-specific lipid transfer protein) genes in the cultivated apple (Malus domestica). Theor Appl Genet 110:479–491PubMedCrossRefGoogle Scholar
  18. Gardiner SE, Bus VGM, Rusholme RL, Chagné D, Rikkerink EHA (2007) Apple. In: Kole C (ed) Fruits and nuts, genome mapping and molecular breeding in plants, vol 4. Springer, Berlin Heidelberg New York, pp 1–62Google Scholar
  19. Gebhardt C, Bellin D, Henselewski H, Lehmann W, Schwarzfischer J, Valkonen JP (2006) Marker-assisted combination of major genes for pathogen resistance in potato. Theor Appl Genet 112:1458–1464PubMedCrossRefGoogle Scholar
  20. Gianfranceschi L, Koller B, Seglias N, Kellerhals M, Gessler C (1996) Molecular selection in apple for resistance to scab caused by Venturia inaequalis. Theor Appl Genet 93:199–204CrossRefGoogle Scholar
  21. 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
  22. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD Markers. Genetics 137:1121–1137PubMedGoogle Scholar
  23. Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R (1997) Microsatellites in Malus × domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94:249–254CrossRefGoogle Scholar
  24. Guo WZ, Zhang TZ, Ding YZ, Zhu YC, Shen XL, Zhu XF (2005) Molecular marker assisted selection and pyramiding of two QTLs for fiber strength in upland cotton. Yi Chuan Xue Bao 32:1275–1285PubMedGoogle Scholar
  25. Harada T, Sunako T, Wakasa Y, Soejima J, Satoh T, Niizeki M (2000) An allele of the 1-aminocyclopropane-1-carboxylate synthase gene (Md-ACS1) accounts for the low level of ethylene production in climacteric fruits of some apple cultivars. Theor Appl Genet 101:742–746CrossRefGoogle Scholar
  26. Hemmat M, Weeden NF, Manganaris AG, Lawson DM (1994) Molecular marker linkage map for apple. J Hered 85:4–11PubMedGoogle Scholar
  27. Horn R, Lecouls A-C, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arús P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419–1428PubMedCrossRefGoogle Scholar
  28. Janssens GA, Goderis IJ, Broekaert WF, Broothaerts W (1995) A molecular method for S-allele identification in apple based on allele-specific PCR. Theor Appl Genet 91:691–698CrossRefGoogle Scholar
  29. 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
  30. King GJ, Maliepaard C, Lynn JR, Alston FH, Durel CE, Evans KM, Griffon B, Laurens F, Manganaris AG, Schrevens E, Tartarini S, 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
  31. King GJ, Lynn JR, Dover CJ, Evans KM, Seymour GB (2001) Resolution of quantitative trait loci for mechanical measures accounting for genetic variation in fruit texture of apple (Malus pumila Mill.). Theor Appl Genet 102:1227–1235CrossRefGoogle Scholar
  32. Klein LG, Way RD, Lamb RC (1961) The inheritance of a lethal factor in apples. Proc Am Soc Hortic Sci 77:50–53Google Scholar
  33. Koller B, Gianfranceschi L, Seglias N, McDermott J, Gessler C (1994) DNA markers linked to Malus floribunda 821 scab resistance. Plant Mol Biol 26:597–602PubMedCrossRefGoogle Scholar
  34. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410PubMedCrossRefGoogle Scholar
  35. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  36. 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 10:217–241CrossRefGoogle Scholar
  37. Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003a) Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theor Appl Genet 106:1497–1508PubMedGoogle Scholar
  38. Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C (2003b) Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Mol Biol 52:511–526PubMedCrossRefGoogle Scholar
  39. Lowe KM, Walker MA (2006) Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) × Riparia Gloire (Vitis riparia). Theor Appl Genet 112:1582–1592PubMedCrossRefGoogle Scholar
  40. 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
  41. Mano Y, Kawasaki S, Takaiwa F, Komatsuda T (2001) Construction of a genetic map of barley (Hordeum vulgare L.) cross ‘Azumamugi’ × ‘Kanto Nakate Gold’ using a simple and efficient amplified fragment-length polymorphism system. Genome 44:284–292PubMedCrossRefGoogle Scholar
  42. Matsumura H, Watanabe S, Harada K, Senda M, Akada S, Kawasaki S, Dubouzet EG, Minaka N, Takahashi R (2005) Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean. Theor Appl Genet 110:1203–1209PubMedCrossRefGoogle Scholar
  43. Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392PubMedCrossRefGoogle Scholar
  44. Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615PubMedCrossRefGoogle Scholar
  45. Niwa Y, Goto K, Shimizu M, Kobayashi H (1997) Chromosomal mapping of genes in the RBCS family in Arabidopsis thaliana. DNA Res 4:341–343PubMedCrossRefGoogle Scholar
  46. Omura M, Ueda T, Kita M, Komatsu A, Takanokura Y, Shimada T, Endo-Inagaki T, Nesumi H, Yoshida T (2000) EST mapping of Citrus. In: Proc Intl Soc Citricult IX Congr. Orlando, FL, pp 71–74Google Scholar
  47. Oraguzie NC, Iwanami H, Soejima J, Harada T, Hall A (2004) Inheritance of the Md-ACS1 gene and its relationship to fruit softening in apple (Malus × domestica Borkh.). Theor Appl Genet 108:1526–1533PubMedCrossRefGoogle Scholar
  48. Patocchi A, Gianfranceschi L, Gessler C (1999a) Towards the map-based cloning of Vf: fine and physical mapping of the Vf region. Theor Appl Genet 99:1012–1017CrossRefGoogle Scholar
  49. Patocchi A, Vinatzer BA, Gianfranceschi L, Tartarini S, Zhang HB, Sansavini S, Gessler C (1999b) Construction of a 550 kb BAC contig spanning the genomic region containing the apple resistance gene Vf. Mol Gen Genet 262:884–891PubMedCrossRefGoogle Scholar
  50. Pearson WR, Wood T, Zhang Z, Miller W (1997) Comparison of DNA sequences with protein sequences. Genomics 46:24–36PubMedCrossRefGoogle Scholar
  51. Saito K, Takeda K (1984) Genetic analysis of resistance to Alternaria Blotch (Alternaria mali Roberts) in apple. (Studies on the breeding of the apple. VIII). Japan J Breed 34:197–209Google Scholar
  52. Sato T, Kudo T, Akada T, Wakasa Y, Niizeki M, Harada T (2004) Allelotype of a ripening-specific 1-aminocyclopropane-1-carboxylate synthase gene defines the rate of fruit drop in apple. J Am Soc Hortic Sci 129:32–36Google Scholar
  53. Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
  54. Staden R, Beal KF, Bonfield JK (2000) The Staden Package. 1998. Methods Mol Biol 132:115–130PubMedGoogle Scholar
  55. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744CrossRefGoogle Scholar
  56. Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker-assisted selection to introgress rice QTLs controlling root traits and aroma into an Indian upland rice variety. Theor Appl Genet 112:208–221PubMedCrossRefGoogle Scholar
  57. Sunako T, Sakuraba W, Senda M, Akada S, Ishikawa R, Niizeki M, Harada T (1999) An allele of the ripening-specific 1-aminocyclopropane-1-carboxylic acid synthase gene (ACS1) in apple fruit with a long storage life. Plant Physiol 119:1297–1303PubMedCrossRefGoogle Scholar
  58. Sung SK, Yu GH, Nam J, Jeong DH, An G (2000) Developmentally regulated expression of two MADS-box genes, MdMADS3 and MdMADS4, in the morphogenesis of flower buds and fruits in apple. Planta 210:519–528PubMedCrossRefGoogle Scholar
  59. 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 apple cultivar ‘Durello di Forlì’. Acta Hortic 663:129–134Google Scholar
  60. Van Ooijen JW, Voortips RE (2001) JoinMap version 3.0, software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  61. Verdoodt L, Van Haute A, Goderis IJ, De Witte K, Keulemans J, Broothaerts W (1998) Use of the multi-allelic self-incompatibility gene in apple to assess homozygocity in shoots obtained through haploid induction. Theor Appl Genet 96:294–300CrossRefGoogle Scholar
  62. Vinatzer BA, Patocchi A, Gianfranceschi L, Tartarini S, Zhang HB, Gessler C, Sansavini S (2001) Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegregating with Vf apple scab resistance. Mol Plant Microbe Interact 14:508–515PubMedCrossRefGoogle Scholar
  63. Voorrips RE (2002) MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78PubMedCrossRefGoogle Scholar
  64. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  65. Wagner DB, Furnier GR, Saghai-Maroof MA, Williams SM, Dancik BP, Allard RW (1987) Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci USA 84:2097–2100PubMedCrossRefGoogle Scholar
  66. Way RD, Lamb RC, Pratt C, Cummins JN (1976) Pale green lethal gene in apple clones. J Am Soc Hortic Sci 101:679–684Google Scholar
  67. Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet 102:865–870CrossRefGoogle Scholar
  68. 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
  69. Yang H, Korban SS (1996) Screening apples for OPD20/600 using sequence-specific primers. Theor Appl Genet 92:263–266CrossRefGoogle Scholar
  70. Yao J-L, Dong Y-H, Kvarnheden A, Morris B (1999) Seven MADS-box genes in apple are expressed in different parts of the fruit. J Am Soc Hortic Sci 124:8–13Google Scholar
  71. You M, Boersma JG, Buirchell BJ, Sweetingham MW, Siddique KH, Yang H (2005) A PCR-based molecular marker applicable for marker-assisted selection for anthracnose disease resistance in lupin breeding. Cell Mol Biol Lett 10:123–134PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Megumi Igarashi
    • 1
  • Yoshie Abe
    • 1
  • Yoshimichi Hatsuyama
    • 1
  • Takanori Ueda
    • 1
  • Tomoko Fukasawa-Akada
    • 2
  • Tomoyuki Kon
    • 2
  • Tsuyoshi Kudo
    • 2
  • Takashi Sato
    • 2
  • Masahiko Suzuki
    • 1
  1. 1.Aomori Green BiocenterAomori Prefectural Agriculture and Forestry Research CenterNogiJapan
  2. 2.Apple Experiment StationAomori Prefectural Agriculture and Forestry Research CenterBotandaira, KuroishiJapan

Personalised recommendations