, Volume 118, Issue 3, pp 281–294 | Cite as

Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids

  • S.C. Hokanson
  • W.F. Lamboy
  • A.K. Szewc-McFadden
  • J.R. McFerson


A collection of 142 accessions of 23 Malus species, derived hybrids and cultivar accessions from the USDA-ARS Plant Genetic Resources Unit's core collection, which represents an extensive range of Malus species, was screened with a set of previously described SSR (simple sequence repeat) markers. The markers were used to determine genetic identities, estimate genetic diversity, identify genetic relationships among the accessions, and determine the utility of SSR primers developed from Malus ×domestica for making genetic assessments across the whole Malus genus. All eight primer pairs amplified multiple fragments when used in polymerase chain reactions with DNA from these accessions. High levels of variation were detected with a mean of 26.4 alleles per locus and a mean direct count heterozygosity across all eight loci equal to 0.623. The eight primer pairs used in this study unambiguously differentiated all but five pairs of accessions in this collection of 142 accessions of 23 Malus species, derived hybrids and cultivars. These SSR data were not useful in identifying genetic relationships among this diverse collection of accessions, with the majority of the accessions not clustering in ways concordant with taxonomic information and/or geographic origin. The resulting phenogram resolved only two meaningful clusters, for the taxonomically isolated Section Chloromeles and for M. fusca accessions, reflecting genetic relationships arising from geographic origin. The detection of identical accessions in the collection, which were previously considered to be unique, highlights the critical need to further bolster collections of certain Malus species.

apple genetic relatedness germplasm management Malus species and hybrids microsatellite markers 


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  1. Aldwinckle, H.S., P.L. Forsline, H.L. Gustafson & S.C. Hokanson, 1997. Evaluation of apple scab resistance of Malus sieversii populations from Central Asia. HortScience 32: 440.Google Scholar
  2. Beckmann, J.S. & M. Soller, 1990. Toward a unified approach to genetic mapping eukaryotes based on sequence tagged microsatellite sites. Bio/Technology 8: 930–932.PubMedCrossRefGoogle Scholar
  3. Briggs, J.B. & F.H. Alston, 1969. Sources of pest resistance in apple cultivars. Rep E Malling Res Stn For 1968: 159–162.Google Scholar
  4. Brooks, H.J. & G. Vest, 1985. Public programs on genetics and breeding of horticultural crops in the United States. HortScience 20: 826–830.Google Scholar
  5. Brown, A.H.D., 1989a. The case for core collections. In: A.H.D. Brown, O.H. Frankel, D.R. Marshall & J.T. Williams (Eds.), The Use of Plant Genetic Resources, pp. 136–156. Cambridge University Press, Cambridge, UK.Google Scholar
  6. Brown, A.H.D., 1995. The core collection at the crossroads. In: T. Hodgkin, A.H.D. Brown, T.J.L. Hintum & E.A.V. Morales (Eds.), Core Collections of Plant Genetic Resources, pp. 319. John Wiley and Sons, Chichester, UK.Google Scholar
  7. Brown, S.K., R.C. Lamb, J.N. Cummins & W.H. Reissig, 1988. Evaluation of Malus germplasm for sources of insect resistance, p. 10. In: International symposium on horticultural germplasm, cultivated and wild. (Abstracts). Chinese Soc Hort Sci Intern Acad Pub, Beijing.Google Scholar
  8. Cregan, P.B., T. Jarvik, A.L. Bush, R.C. Shoemaker, K.G. Lark, A.L. Kahler, N. Kaya, T.T. VanToai, D.G. Lohnes, J. Chung & J.E. Sprecht, 1999. An integrated genetic linkage map of the soybean genome. Crop Science 39: 1464–1490.CrossRefGoogle Scholar
  9. Cummins, J.N. & H.S. Aldwinckle, 1980. Breeding tree crops. In: M.K. Harris (Ed.), Biology and Breeding for Resistance to Arthropods and Pathogens in Horticultural Plants, pp. 528–545. Texas A and M Univ, College Station, TX.Google Scholar
  10. Cummins, J.N., 1983a. Rootstock breeding. In: J.N. Moore & J. Janick (Eds.), Methods in Fruit Breeding, pp. 294–327. Purdue Univ Press, W. Lafayette, IN.Google Scholar
  11. Cummins, J.N., 1983b. Breeding apple rootstocks. Plant Breeding Rev 1: 294–394.Google Scholar
  12. Dabrowski, Z.T. & A. Rejman, 1975. Some aspects of host plant relationships of the fruit tree red spider mite, Panonychus ulmi (Koch). Zeszyty Probl Post Nauk Roln 171: 73–79.Google Scholar
  13. Dayton, D.F. & E.B. Williams, 1968. Independent genes in Malus for resistance to Venturia inaequalis. Proc Am Soc Hort Sci 92: 89–94.Google Scholar
  14. Dayton, D.F. & E.B. Williams, 1970. Additional allelic genes in Malus for scab resistance of two reaction types. J Am Soc Hort Sci 95: 735–736.Google Scholar
  15. Dunemann, F., R. Kahnau & H. Schmidt, 1994. Genetic relationships in Malus evaluated by RAPD ‘fingerprinting’ of cultivars and wild species. Plant Breeding 113: 150–159.CrossRefGoogle Scholar
  16. Ellegren, H., C.R. Primmer & B.C. Sheldon, 1995. Microsatellite evolution: Directionality or bias? Nature Genet 11: 36–362.CrossRefGoogle Scholar
  17. Food and Agriculture Organization, 1997. FAOSTAT database collections. Rome, Italy. pl?subset=agriculture.Google Scholar
  18. Forsline, P.L., 2000. Procedures for collection, conservation, evaluation and documentation of germplasm using Malus as an example. Acta Hort 522: 223–234.Google Scholar
  19. Forsline, P.L., 1992. Core subsets in the USDA/NPGS with apple as an example. In: C.G. Davidson & J. Warner (Eds.), Proceedings of the 2nd Workshop on Clonal Genetic Resources: Emerging Issues and New Directions, pp. 172–175. Canadian Agriculture Research Council, Ottawa, Canada.Google Scholar
  20. Forsline, P.L. & R.D. Way, 1993. Apple accessions of low priority targeted for removal from the National Plant Germplasm System. Fruit Var Jour 47: 204–214.Google Scholar
  21. Frankel, O.H., 1984. Genetic perspectives of germplasm conservation. In: W. Arber, K. Llimensee, W.J. Peacock & P. Starlinger (Eds.), Genetic Manipulation: Impact on Man and Society. Cambridge University Press, Cambridge, UK.Google Scholar
  22. Frey, K.J., 1996. National plant breeding study-I. Human and financial resources devoted to plant breeding research and development in the United States in 1994. Special Report 98. Iowa Agriculture and Home Economics Experiment Station. Ames, IA.Google Scholar
  23. Gardner, R., J.N. Cummins & H.S. Aldwinckle, 1980. Inheritance of fire blight resistance in Malus in relation to rootstock breeding. J Amer Soc HortSci 105: 912–916.Google Scholar
  24. Garza, J.C., M. Slatkin & N.B. Freimer, 1995. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol Biol Evol 12: 594–603.PubMedGoogle Scholar
  25. Gianfranceschi, L., N. Seglias, R. Tarchini, M. Komjanc & C. Gessler, 1998. Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet 96: 1069–1076.CrossRefGoogle Scholar
  26. Goldstein, D.B. & D.D. Pollock, 1997. Launching microsatellites: A review of mutation processes and methods of phylogenetic inference. J Hered 88: 335–342.PubMedGoogle Scholar
  27. Goonewardene, H.F., 1987. E11–24, E14–32 and E36–7 apple germplasm with multiple pest resistance. HortScience 22: 1346–1348.Google Scholar
  28. Goonewardene, H.F. & P.H. Howard, 1989. E7–47, E7–54, E29–56, and E31–10 apple germplasm with multiple pest resistance. HortScience 24: 167–169.Google Scholar
  29. Hemmat, M., N.F. Weeden, A.K. Szewc-McFadden & S.C. Hokanson, 1998. Mapping of Malus domestica microsatellites in apple and pear. (Abstr.), pp. 148. Proceedings Plant and Animal Genome V, January 12–16, 1997, San Diego, CA.Google Scholar
  30. Hokanson, S.C., A.K. Szewc-McFadden, W.F. Lamboy & J.R. McFerson, 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus × domestica Borkh. core subset collection. Theor Appl Genet 97: 671–683.CrossRefGoogle Scholar
  31. Hokanson, S.C., J.R. McFerson, P.L. Forsline, W.F. Lamboy, J.J. Luby, H.S. Aldwinckle & A.D. Djangaliev, 1997. Collecting and managing wild Malus germplasm in its center of diversity. HortScience 32: 173–176.Google Scholar
  32. Hough, L.F., J.R. Shay & D.F. Dayton, 1953. Apple scab resistance from Malus floribunda Sieb. Proc Am Soc Hort Sci 62: 341–347.Google Scholar
  33. Huckins, C.A., 1972. A revision of the sections of the genus Malus Miller. Ph.D. Thesis, Cornell University, Ithaca, NY.Google Scholar
  34. Janick, J., 1974. The apple in Java. HortScience 9: 13–15.Google Scholar
  35. Janick, J., J.N. Cummins, S.K. Brown & M. Hemmat, 1996. Apples. In: J. Janick & J.N. Moore (Eds.), Fruit breeding. vol. II. Tree and Tropical Fruits, pp. 1–76. Wiley, New York.Google Scholar
  36. Jones, D.A., 1972. Blood samples: Probability of discrimination. J Forens Sci Soc 12: 355–359.CrossRefGoogle Scholar
  37. King, G.J., 1996. Progress of apple genetic mapping in Europe. HortScience 31: 1108–1111.Google Scholar
  38. Kloosterman, A.D., B. Budowle & P. Daselaar, 1993. PCRamplification and detection of the human D1S80 VNTR locus. Int J Leg Med 105: 257–264.CrossRefGoogle Scholar
  39. Knight, R.L. & F.H. Alston, 1968. Sources of field immunity to mildew (Podosphaera leucotricha). Can J Gen Cytol 10: 294–298.Google Scholar
  40. Korban, S.S., 1986. Interspecific hybridization in Malus. HortScience 21: 41–48.Google Scholar
  41. Kresovich, S., W.F. Lamboy, J.R. McFerson & P.L. Forsline, 1995. Integrating different types of information to develop core collections, with particular reference to Brassica oleracea and Malus x domestica. In: T. Hodgkin, A.H.D. Brown, T.J.L. Hintum & E.A.V. Morales (Eds.), Core Collections of Plant Genetic Resources, pp. 147–154. John Wiley and Sons, Chichester, UK.Google Scholar
  42. Lamboy, W.F. & C.G. Alpha, 1998. Using simple sequence repeats (SSRs) for DNA fingerprinting germplasm accessions of grape (Vitis L.) species. J Am Soc Hortic Sci 123: 182–188.Google Scholar
  43. Langenfeld, W.T., 1991. Apple trees. Morphological evolution, phylogeny, geography and systematics. Riga (Zinatne) 232. (In Russian).Google Scholar
  44. Lapkins, K.O., 1969. Segregation of compact growth types in certain apple seedling progenies. Can J Pl Sci 49: 765–768.CrossRefGoogle Scholar
  45. Lapkins, K.O., 1976. Inheritance of compact growth type in apple. J Am Soc Hort Sci 101: 133–135.Google Scholar
  46. Li, Y., 1996. A critical review of the species and the classification of the genus Malus Mill. in the world. Journal of Fruit Science, Vol. 10 (Suppl.) Zhengzhou Fruit Research Institute, pp. 63–81. (In Chinese).Google Scholar
  47. Maliepaard, C., F.H. Alston, G. van Arkel, L.M. Brown, E. Chevreau, F. Dunemann, K.M. Evans, S. Gardiner, P. Guilford, A.W. van Heusden, J. Janse, F. Laurens, J.R. Lynn, A.G. Manganaris, A.P.M. den Nijs, N. Periam, E. Rikkerink, P. Roche, C. Ryder, S. Sansavini, H. Schmidt, S. Tartarini, J.J. Verhaegh, M. Vrielinkvan Ginkel & G.J. King, 1998. Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97: 60–73.CrossRefGoogle Scholar
  48. Marshall, D.R., 1990. Crop genetic resources: Current and emerging issues. In: A.H.D. Brown, M.H. Clegg, A.L. Kahler & B.S. Weir (Eds.), Plant Population Genetics, Breeding, and Genetic Resources, pp. 367–388. John Wiley and Sons, Chichester, UK.Google Scholar
  49. Meulenbroek, B., J. Verhaegh & J. Janse, 1999. Inheritance studies with columnar type trees. Acta Hort 484: 255–259.Google Scholar
  50. Momol, M.T., P.L. Forsline, W.F. Lamboy & H.S. Aldwinckle, 1999. Fire blight resistance and horticultural evaluation of wild Malus populations from Central Asia. Acta Hort 489: 229–234.Google Scholar
  51. Nei, M., 1972. Genetic distance between populations. Am Nat 106: 283–292.CrossRefGoogle Scholar
  52. Noiton, D.A.M. & P.A. Alspach, 1996. Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Soc Hortic Sci 121: 773–782.Google Scholar
  53. Ragan, W.H., 1926. Nomenclature of the apple: a catalogue index of the known varieties referred to in American publications from 1804 to 1904. USDA Bur Plant Ind Bul 56.Google Scholar
  54. Rehder, A., 1940. Manual of cultivated trees and shrubs. Ed. 2. Macmillan, New York.Google Scholar
  55. Röder, M.S., J. Plaschke, S.U. König, A. Börner, M.E. Sorrells, S.D. Tanksley & M.W. Ganal, 1995. Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246: 327–333.PubMedCrossRefGoogle Scholar
  56. Rohlf, F.J., 1998. NTSYS-pc, numerical taxonomy and multivariate analysis system, version 2.01. Exeter Publishing, Ltd., Setauket, New York.Google Scholar
  57. Sax, K., 1959. The cytogenetics of facultative apomixis in Malus species. Journal of the Arnold Arboretum 40: 289–297.Google Scholar
  58. Sneath, P.H.A. & R.R. Sokal, 1973. Numerical Taxonomy. W.H. Freeman and Co., San Francisco, CA.Google Scholar
  59. Stepanov, S.N., 1974. Species and forms of fruit trees and bushes of the USSR and their utilization in plant breeding. Proc. 19th Intl. Hort. Congr., Warsaw 2: 1–12.Google Scholar
  60. Strang, J.G. & C. Stushnoff, 1975. A classification of hardy North American apple cultivars based on hardiness zones. Fruit Var J 29: 78–108.Google Scholar
  61. Szewc-McFadden, A.K., S. Bleik, C.G. Alpha, W.F. Lamboy & J.R. McFerson, 1995. Identification of simple sequence repeats in Malus (Apple). HortScience 30: 855.Google Scholar
  62. Szewc-McFadden, A.K., W.F. Lamboy, S.C. Hokanson & J.R. McFerson, 1996. Utilization of identified simple sequence repeats (SSRs) in Malus x domestica (Apple) for germplasm characterization. HortScience 31: 619.Google Scholar
  63. Tanksley, S.D. & J.C. Nelson, 1996. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92: 191–203.CrossRefGoogle Scholar
  64. van der Zwet, T. & H.L. Keil, 1979. Fireblight. USDA Hdbk. No. 510. U.S. Govt. Printing Office, Washington, D.C.Google Scholar
  65. Walter, K.S. & H.J. Gillett, 1998. 1997 IUCN Red List of Threatened Plants. Compiled by the World Conservation Monitoring Centre. IUCN - The World Conservation Union, Gland, Switzerland and Cambridge, UK.Google Scholar
  66. Watkins, R., 1973. Fruit Breeding. Annu. Rpt. E. Malling Res. Sta. 1972. pp. 134–136.Google Scholar
  67. Watkins, R., 1981. The main species of Malus. In: B. Hora (Ed.), The Oxford Encyclopedia of Trees of the World, pp. 188–192. Oxford Univ. Press, Oxford.Google Scholar
  68. Way, R.D., H.S. Aldwinckle, R.C. Lamb, A. Rejman, S. Sansavini, T. Shen, R. Watkins, M.N. Westwood & Y. Yoshida, 1991. Apples (Malus). In: J.N. Moore & J.R. Ballington (Eds.), Genetic Resources of Temperate Fruit and Nut Crops 1, pp. 3–62. Intl Soc Hort Sci, Wageningen, Netherlands.Google Scholar
  69. Weber, J.L., 1990. Human DNA polymorphisms and methods of analysis. Curr Opin Biotechnol 1: 166–171.PubMedCrossRefGoogle Scholar
  70. Weir, B.S., 1989. Sampling properties of gene diversity. In: A.H.D. Brown M.T. Clegg, H.L. Kahler & B.S. Weir (Eds.), Plant Population Genetics, Breeding and Genetic Resources. Sinauer Associates, Sunderland, Mass, pp. 23–42.Google Scholar
  71. Williams, E.B. & J. Kuc, 1969. Resistance in Malus to Venturia inaequalis. Ann Rev Phytopath 7: 223–246.CrossRefGoogle Scholar
  72. Xiao, J., S. Grandillo, S.N. Ahn, S.R. McCouch & S.D. Tanksley, 1996. Genes from wild rice improve yield. Nature 384: 223–224.CrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • S.C. Hokanson
    • 1
  • W.F. Lamboy
    • 2
  • A.K. Szewc-McFadden
    • 2
  • J.R. McFerson
    • 3
  1. 1.USDA-ARS Fruit LabBeltsvilleU.S.A.
  2. 2.USDA-ARS Plant Genetic Resources UnitCornell UniversityGenevaU.S.A.
  3. 3.Washington Tree Fruit Research CommissionWenatcheeU.S.A.

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