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Genetics, Vol. 168, 1019-1027, October 2004, Copyright © 2004
doi:10.1534/genetics.104.030296
Multiple Quantitative Trait Loci Mapping With Cofactors and Application of Alternative Variants of the False Discovery Rate in an Enlarged Granddaughter Design
Jörn Bennewitz*,1,
Norbert Reinsch
,
Volker Guiard,
Sebastien Fritz
,
Hauke Thomsen
,
Christian Looft*,
Christa Kühn,
Manfred Schwerin,
Christina Weimann**,
Georg Erhardt**,
Fritz Reinhardt,
Reinhard Reents,
Didier Boichard and
Ernst Kalm*
* Institute of Animal Breeding and Husbandry, University of Kiel, D-24098 Kiel, Germany
Research Institute for the Biology of Farm Animals, D-18196 Dummerstorf, Germany
UNCEIA, 75595 Paris 12, France
United Datasystems for Animal Production (VIT), D-27283 Verden/Aller, Germany
Station de Génétique Quantitative et Appliquée, INRA, 78352 Jouy en Josas, France
** Institute of Animal Breeding and Genetics, University Giessen, D-35390 Giessen, Germany
1 Corresponding author: Institute of Animal Breeding and Husbandry, University of Kiel, D-24098 Kiel, Germany.
E-mail: jbennewitz{at}tierzucht.uni-kiel.de
The experimental power of a granddaughter design to detect quantitative trait loci (QTL) in dairy cattle is often limited by the availability of progeny-tested sires, by the ignoring of already identified QTL in the statistical analysis, and by the application of stringent experimentwise significance levels. This study describes an experiment that addressed these points. A large granddaughter design was set up that included sires from two countries (Germany and France), resulting in almost 2000 sires. The animals were genotyped for markers on nine different chromosomes. The QTL analysis was done for six traits separately using a multimarker regression that included putative QTL on other chromosomes as cofactors in the model. Different variants of the false discovery rate (FDR) were applied. Two of them accounted for the proportion of truly null hypotheses, which were estimated to be 0.28 and 0.3, respectively, and were therefore tailored to the experiment. A total of 25 QTL could be mapped when cofactors were included in the model—7 more than without cofactors. Controlling the FDR at 0.05 revealed 31 QTL for the two FDR methods that accounted for the proportion of truly null hypotheses. The relatively high power of this study can be attributed to the size of the experiment, to the QTL analysis with cofactors, and to the application of an appropriate FDR.
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