Linkage disequilibrium on the bovine X chromosome: characterization and use in quantitative trait locus mapping.
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.
Sandor
Cynthia
C
Unit of Animal Genomics, Department of Animal Producion, University of Liège, Belgium.
Farnir
Frédéric
F
Hansoul
Sarah
S
Coppieters
Wouter
W
Meuwissen
Théo
T
Georges
Michel
M
D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D015810:Linkage Disequilibrium; D008297:Male; D008390:Markov Chains; D010375:Pedigree; D010641:Phenotype; D040641:Quantitative Trait Loci; D014960:X Chromosome