Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design.

Authors:
Norbert Reinsch
Norbert Reinsch
Institute of Genetics and Biometry
Sebastien Fritz
Sebastien Fritz
University of Kiel
Germany
Hauke Thomsen, Dr.
Hauke Thomsen, Dr.
GeneWerk GmbH
Senior Bioinformatician
Bioinformatics, Biostatistics, Genetics
Heidelberg, Baden-Württemberg/Germany | Germany
Christian Looft
Christian Looft
Institute of Animal Science
Blacksburg | United States
Manfred Schwerin
Manfred Schwerin
Research Institute for the Biology of Farm Animals
Germany

Genetics 2004 Oct;168(2):1019-27

Institute of Animal Breeding and Husbandry, University of Kiel, D-24098 Kiel, Germany.

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.

Download full-text PDF

Source
http://www.genetics.org/cgi/doi/10.1534/genetics.104.030296
Publisher Site
http://dx.doi.org/10.1534/genetics.104.030296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448815PMC

Still can't find the full text of the article?

We can help you send a request to the authors directly.
October 2004
10 Reads

Publication Analysis

Top Keywords

granddaughter design
12
qtl analysis
8
variants false
8
false discovery
8
null hypotheses
8
accounted proportion
8
proportion null
8
cofactors application
8
discovery rate
8
quantitative trait
8
trait loci
8
qtl
7
cofactors
5
putative qtl
4
included putative
4
separately multimarker
4
multimarker regression
4
qtl chromosomes
4
regression included
4
model variants
4

Similar Publications