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Originally published as Genetics Published Articles Ahead of Print on April 30, 2006.
Genetics, Vol. 173, 1777-1786, July 2006, Copyright © 2006
doi:10.1534/genetics.106.059329
Linkage Disequilibrium on the Bovine X Chromosome: Characterization and Use in Quantitative Trait Locus Mapping
Cynthia Sandor*,
Frédéric Farnir*,
Sarah Hansoul*,
Wouter Coppieters*,
Théo Meuwissen
and
Michel Georges*,1
* Unit of Animal Genomics, Department of Animal Production, Faculty of Veterinary Medicine and CBIG, University of Liège, 4000 Liège, Belgium and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Aas, Norway
1 Corresponding author: Unit of Animal Genomics, Faculty of Veterinary Medicine and CBIG, University of Liège (B43), 20 Blvd. de Colonster, 4000 Liège, Belgium.
E-mail: michel.georges{at}ulg.ac.be
We herein demonstrate that in the Holstein–Friesian dairy cattle population, microsatellites are as polymorphic on the X chromosome as on the autosomes but that the level of linkage disequilibrium between these markers is higher on the X chromosome than on the autosomes. The latter observation is not compatible with the small male-to-female ratio that prevails in this population and results in a higher gonosomal than autosomal effective population size. It suggests that the X chromosome undergoes distinct selective or mutational forces. We describe and characterize a novel Markovian approach to exploit this linkage disequilibrium to compute the probability that two chromosomes are identical-by-descent conditional on flanking marker data. We use the ensuing probabilities in a restricted maximum-likelihood approach to search for quantitative trait loci (QTL) affecting 48 traits of importance to the dairy industry and provide evidence for the presence of QTL affecting 5 of these traits on the bovine X chromosome.
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