title: Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design.
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 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.
authors.affiliation: Institute of Animal Breeding and Husbandry, University of Kiel, D-24098 Kiel, Germany. jbennewitz@tierzucht.uni-kiel.de
authors.forename: Jörn
authors.initials: J
authors.lastname: Bennewitz
authors.forename: Norbert
authors.initials: N
authors.lastname: Reinsch
authors.forename: Volker
authors.initials: V
authors.lastname: Guiard
authors.forename: Sebastien
authors.initials: S
authors.lastname: Fritz
authors.forename: Hauke
authors.initials: H
authors.lastname: Thomsen
authors.forename: Christian
authors.initials: C
authors.lastname: Looft
authors.forename: Christa
authors.initials: C
authors.lastname: Kühn
authors.forename: Manfred
authors.initials: M
authors.lastname: Schwerin
authors.forename: Christina
authors.initials: C
authors.lastname: Weimann
authors.forename: Georg
authors.initials: G
authors.lastname: Erhardt
authors.forename: Fritz
authors.initials: F
authors.lastname: Reinhardt
authors.forename: Reinhard
authors.initials: R
authors.lastname: Reents
authors.forename: Didier
authors.initials: D
authors.lastname: Boichard
authors.forename: Ernst
authors.initials: E
authors.lastname: Kalm
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003612:Dairying; D005189:False Positive Reactions; D005260:Female; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D008297:Male; D018895:Microsatellite Repeats; D010375:Pedigree; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers