Theoretical and Applied Genetics

, Volume 109, Issue 2, pp 402–408 | Cite as

Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method

  • G. D. Esselink
  • H. NybomEmail author
  • B. Vosman
Original Paper


Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting—peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose (Rosa × hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting ‘null’ alleles in polyploid species.


Peak Ratio Polyploid Species Polyploid Plant STMS Marker Allelic Configuration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Financial support was received from the Erik Philip-Sörensen Foundation and the Commission of the European Communities, specific Research programme ‘Quality of Life and Management of Living Resources’, QLRT-2001-01278 ‘Genetic evaluation of European rose resources for conservation and horticultural use’. It does not necessarily reflect its views and in no way anticipates the Commission’s future policy in this area.


  1. Amsellem L, Dutech C, Billotte N (2001) Isolation and characterization of polymorphic microsatellite loci in Rubus alceifolius Poir. (Rosaceae), an invasive weed in La Réunion island. Mol Ecol Notes 1:33–35Google Scholar
  2. Andrew RL, Miller JT, Peakall R, Crips MD, Bayer RJ (2003) Genetic, cytogenetic and morphological patterns in a mixed mulga population: evidence for apomixis. Aust Syst Bot 16:69–80CrossRefGoogle Scholar
  3. Ashley MV, Wilk JA, Styan SMN, Craft KJ, Jones KL, Feldheim KA, Lewers KS, Ashman TL (2003) High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae). Theor Appl Genet 107:1201–1207CrossRefPubMedGoogle Scholar
  4. Becher SA, Steinmetz K, Weising K, Boury S, Peltier D, Renou J-P, Kahl G, Wolff K (2000) Microsatellites for cultivar identification in Pelargonium. Theor Appl Genet 101:643–651CrossRefGoogle Scholar
  5. Bockelmann A-C, Reusch TBH, Bijlsma R, Bakker JP (2003) Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes. Mol Ecol 12:505–515CrossRefPubMedGoogle Scholar
  6. Cai H-W, Yuyama N, Tamaki H, Yoshizawa A (2003) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.). Theor Appl Genet 107:1337–1349CrossRefPubMedGoogle Scholar
  7. Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR (1993) Incidence and origin of ‘null’ alleles in the (AC)n microsatellite markers. Am J Hum Genet 52:922–927Google Scholar
  8. Esselink GD, Smulders MJM, Vosman B (2003) Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 106:277–286PubMedGoogle Scholar
  9. Falque M, Keurentjes J, Bakx-Schotman JMT, van Dijk PJ (1998) Development and characterization of microsatellite markers in the sexual-apomictic complex Taraxacum officinale (dandelion). Theor Appl Genet 97:283–292Google Scholar
  10. Huang W-G, Cipriani G, Morgante M, Testolin R (1998) Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species. Theor Appl Genet 97:1269–1278CrossRefGoogle Scholar
  11. Lerceteau-Köhler E, Guérin G, Laigret F, Denoyes-Rothan B (2003) Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria x ananassa) using AFLP mapping. Theor Appl Genet 107:619–628CrossRefPubMedGoogle Scholar
  12. Lian C, Nara K, Nakaya H, Zhou Z, Wu B, Miyashita N, Hogetsu T (2001) Development of microsatellite markers in polyploid Salix reinii. Mol Ecol Notes 1:160–161CrossRefGoogle Scholar
  13. 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 10:217–241Google Scholar
  14. Macaferri M, Sanguineti MC, Donini T, Tuberosa R (2003) Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor Appl Genet 107:783–797CrossRefPubMedGoogle Scholar
  15. Masterson J (1994) Stomatal size in fossils: evidence for polyploidy in majority of angiosperms. Science 264:421–424Google Scholar
  16. McGregor CE, Lambert CA, Greyling MM, Louw JH, Warnich L (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144CrossRefGoogle Scholar
  17. Mengoni A, Gori A, Bazzicalupo M (2000) Use of RAPD and microsatellite (SSR) variation to assess genetic relationships among populations of tetraploid alfalfa, Medicago sativa. Plant Breed 119:311–317Google Scholar
  18. Nybom H, Esselink GD, Werlemark G, Vosman B (2004) Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dogroses, Rosa L. sect. Caninae. Heredity 92:139–150CrossRefPubMedGoogle Scholar
  19. Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084Google Scholar
  20. Soltis DE, Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14:348–352PubMedGoogle Scholar
  21. Soltis DE, Soltis PS (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA 97:7015–7057CrossRefGoogle Scholar
  22. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22:130–138PubMedGoogle Scholar
  23. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83:294–300Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Department of Biodiversity and BreedingPlant Research InternationalWageningenThe Netherlands
  2. 2.Balsgård-Department of Crop ScienceSwedish University of Agricultural SciencesKristianstadSweden

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