Advertisement

Theoretical and Applied Genetics

, Volume 112, Issue 1, pp 187–194 | Cite as

SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data

  • Hans van Os
  • Piet Stam
  • Richard G. F. Visser
  • Herman J. van Eck
Original Paper

Abstract

High-density genetic linkage maps can be used for purposes such as fine-scale targeted gene cloning and anchoring of physical maps. However, their construction is significantly complicated by even relatively small amounts of scoring errors. Currently available software is not able to solve the ordering ambiguities in marker clusters, which inhibits the application of high-density maps. A statistical method named SMOOTH was developed to remove genotyping errors from genetic linkage data during the mapping process. The program SMOOTH calculates the difference between the observed and predicted values of data points based on data points of neighbouring loci in a given marker order. Highly improbable data points are removed by the program in an iterative process with a mapping algorithm that recalculates the map after cleaning. SMOOTH has been tested with simulated data and experimental mapping data from potato. The simulations prove that this method is able to detect a high amount of scoring errors and demonstrates that the program enables mapping software to successfully construct a very accurate high-density map. In potato the application of the program resulted in a reliable placement of nearly 1,000 markers in one linkage group.

Keywords

High-density genetic linkage maps Software Simulations Scoring errors 

Notes

Acknowledgements

We are very grateful to Dr. Fred van Eeuwijk for providing valuable comments. This work was carried out under the EU FAIR programme grant: FAIR5-PL97-3565.

References

  1. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedPubMedCentralGoogle Scholar
  2. Isidore E, Van Os H, Andrzejewski S, Bakker J, Barrena I, Bryan GJ, Caromel B, Van Eck H, Ghareeb B, De Jong W, Van Koert P, Lefebvre V, Milbourne D, Ritter E, Rouppe van der Voort J, Rousselle-Bourgeois F, Van Vliet J, Waugh R (2003) Toward a marker-dense meiotic map of the potato genome: Lessons from linkage group I. Genetics 165:2107–2116PubMedPubMedCentralGoogle Scholar
  3. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE (2000) A high-throughput aflp-based method for constructing integrated genetic and physical maps: progress towards a sorghum genome map. Genome Res 10:789–807CrossRefPubMedPubMedCentralGoogle Scholar
  4. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  5. Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604–610CrossRefPubMedGoogle Scholar
  6. Nilsson NO, Säll T, Bengtsson BO (1993) Chiasma and recombination data in plants: are they compatible?. Trends Genet 9:344–348CrossRefPubMedGoogle Scholar
  7. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744CrossRefGoogle Scholar
  8. Stam P, Van Ooijen JW (1995) JoinMap™ version 2.0: Software for the calculation of genetic linkage maps. CPRO-DLO, WageningenGoogle Scholar
  9. Strommer J, Peters J, Zethof J, De Keukeleire P, Gerats T (2002) AFLP maps of Petunia hybrida: building maps when markers cluster. Theor Appl Genet 105:1000–1009CrossRefPubMedGoogle Scholar
  10. Van Os H, Stam P, Visser RGF, Van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet (in press and aiming for back-to-back publication)Google Scholar
  11. 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 23:4407–4414CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Hans van Os
    • 1
  • Piet Stam
    • 1
  • Richard G. F. Visser
    • 1
  • Herman J. van Eck
    • 1
  1. 1.Laboratory of Plant BreedingWageningen UniversityWageningenThe Netherlands

Personalised recommendations