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Estimation and test for linkage between markers: a comparison of lod score and χ 2 test in a linkage study of maritime pine (Pinus pinaster Ait.)

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Abstract

The first step in the construction of a linkage map involves the estimation and test for linkage between all possible pairs of markers. The lod score method is used in many linkage studies for the latter purpose. In contrast with classical statistical tests, this method does not rely on the choice of a first-type error level. We thus provide a comparison between the lod score and a χ 2 test on linkage data from a gymnosperm, the maritime pine. The lod score appears to be a very conservative test with the usual thresholds. Its severity depends on the type of data used.

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Authors and Affiliations

  1. ESV, bât 362, F-91405, Orsay Cedex, France

    S. Gerber

  2. Laboratoire de Biometrie, INRA, F-78370, Jouy en Josas, France

    F. Rodolphe

Authors
  1. S. Gerber
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  2. F. Rodolphe
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Communicated by P. M. A. Tigerstedt

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Gerber, S., Rodolphe, F. Estimation and test for linkage between markers: a comparison of lod score and χ 2 test in a linkage study of maritime pine (Pinus pinaster Ait.). Theoret. Appl. Genetics 88, 293–297 (1994). https://doi.org/10.1007/BF00223635

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  • DOI: https://doi.org/10.1007/BF00223635

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