Theoretical and Applied Genetics

, Volume 125, Issue 7, pp 1393–1402 | Cite as

Three-point appraisal of genetic linkage maps

  • W. R. GilksEmail author
  • S. J. Welham
  • J. Wang
  • S. J. Clark
  • G. J. King
Original Paper


This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8–12 cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped.


Linkage Group Posterior Probability Doubled Haploid Marker Order High Posterior Probability 
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.



The authors are funded by the UK Biotechnology & Biological Sciences Research Council (BBSRC) with project funding to GJK and JW under BBE0177971, and SJW and GJK from Department for Environment Food and Rural Affairs project IF0144 (OREGIN). We would like to thank Jonathan Myles for wrapping our R functions into a package, and two anonymous referees for comments which led to improvements in the algorithm, paper and interpretation of our method.


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • W. R. Gilks
    • 1
    • 2
    Email author
  • S. J. Welham
    • 1
    • 3
  • J. Wang
    • 4
    • 5
  • S. J. Clark
    • 1
  • G. J. King
    • 4
    • 6
  1. 1.Department of Computational and Systems BiologyRothamsted ResearchHarpendenUK
  2. 2.Department of Statistics, School of MathematicsUniversity of LeedsLeedsUK
  3. 3.VSN International LtdHemel HempsteadUK
  4. 4.Plant Sciences, Rothamsted ResearchHarpendenUK
  5. 5.Centre for Haemato-Oncology, Institute of CancerBarts and the London School of Medicine and DentistryLondonUK
  6. 6.Southern Cross Plant ScienceSouthern Cross UniversityLismoreAustralia

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