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Aspects of maximum likelihood methods for the mapping of quantitative trait loci in line crosses

Published online by Cambridge University Press:  14 April 2009

S. A. Knott  and
C. S. Haley
S. A. Knott*
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT
C. S. Haley
Affiliation:
AFRC Institute of Animal Physiology and Genetics Research, Edinburgh Research Station, Roslin, Midlothian, EH25 9PS
*
*Corresponding author.
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Summary

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Maximum likelihood methods for the mapping of quantitative trait loci (QTL) have been investigated in an F2 population using simulated data. The use of adjacent (flanking) marker pairs gave improved power for the detection of QTL over the use of single markers when markers were widely spaced and the QTL effect large. The use of flanking marker loci also always gave moreaccurate and less biassed estimates for the effect and position of the QTL and made the method less sensitive to violations of assumptions, for example non-normality of the distribution. Testing the hypothesis of a linked QTL against that of no QTL is not biassed by the presence of unlinked QTL. This test is more robust and easier to obtain than the comparison of a linked with an unlinked QTL. Fixing the recombination fraction between the markers at an incorrect value in the analyses with flanking markers does not generally bias the test for QTL or estimates of their effect. The presence of multiple linked QTL bias both tests and estimates of effect with interval mapping, leading to inflated values when QTL are in association in the lines crossed and deflated values when they are in dispersion.

Type
Research Article
Information
Genetics Research , Volume 60 , Issue 2 , October 1992 , pp. 139 - 151
Copyright
Copyright © Cambridge University Press 1992

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