Advanced

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

Bennewitz, Jörn ; Reinsch, Norbert ; Guiard, Volker ; Fritz, Sebastien ; Thomsen, Hauke LU ; Looft, Christian ; Kühn, Christa ; Schwerin, Manfred ; Weimann, Christina and Erhardt, Georg , et al. (2004) In Genetics 168(2). p.1019-1027
Abstract

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... (More)

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.

(Less)
Please use this url to cite or link to this publication:
author
, et al. (More)
(Less)
publishing date
type
Contribution to journal
publication status
published
in
Genetics
volume
168
issue
2
pages
1019 - 1027
publisher
Genetics Society of America
external identifiers
  • scopus:8544233572
  • pmid:15514072
ISSN
0016-6731
DOI
10.1534/genetics.104.030296
language
English
LU publication?
no
id
57bbbc16-51a9-43e9-8880-d352cec450ed
date added to LUP
2018-10-10 13:36:03
date last changed
2020-01-13 01:02:21
@article{57bbbc16-51a9-43e9-8880-d352cec450ed,
  abstract     = {<p>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.</p>},
  author       = {Bennewitz, Jörn and Reinsch, Norbert and Guiard, Volker and Fritz, Sebastien and Thomsen, Hauke and Looft, Christian and Kühn, Christa and Schwerin, Manfred and Weimann, Christina and Erhardt, Georg and Reinhardt, Fritz and Reents, Reinhard and Boichard, Didier and Kalm, Ernst},
  issn         = {0016-6731},
  language     = {eng},
  month        = {10},
  number       = {2},
  pages        = {1019--1027},
  publisher    = {Genetics Society of America},
  series       = {Genetics},
  title        = {Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design},
  url          = {http://dx.doi.org/10.1534/genetics.104.030296},
  doi          = {10.1534/genetics.104.030296},
  volume       = {168},
  year         = {2004},
}