title: Genome-wide linkage disequilibrium in the Blonde d'Aquitaine cattle breed.
abstract: We present here the first genome-wide characterization of linkage disequilibrium (LD) in the French Blonde d'Aquitaine (BLA) breed, a well-muscled breed renowned for producing high-yielding beef carcasses. To assess the pattern and extent of LD, we used a sample of 30 unrelated bulls and 36 923 single nucleotide polymorphisms (SNPs) covering all cattle autosomes. The squared correlation of the alleles at two loci (r(2) ) was used as a measure of LD. The analysis of adjacent marker pairs revealed that the level of LD decreases rapidly with physical distance between SNPs. Overall mean r(2) was 0.205 (±0.262). Strong LD (r(2)  > 0.8) and useful LD (measured as r(2 ) > 0.2) were observed within genomic regions of up to 720 and 724 kb, respectively. We analysed the genetic structure of the BLA population and found stratification. The observed genetic sub-structuring is consistent with the known recent demographic history that occurred during BLA breed formation. Our results indicate that LD mapping of phenotypic traits in the BLA population is feasible; however, because of this sub-structuring, special care is needed to reduce the likelihood of false-positive associations between marker loci and traits of interest.
authors.affiliation: Undergraduate Programme in Bioinformatics, Institut Universitaire Technologique d'Aurillac/Université d'Auvergne, Jouy-en-Josa, France; INRA/AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josa, France.
authors.forename: J
authors.initials: J
authors.lastname: Beghain
authors.forename: S
authors.initials: S
authors.lastname: Boitard
authors.forename: B
authors.initials: B
authors.lastname: Weiss
authors.forename: M
authors.initials: M
authors.lastname: Boussaha
authors.forename: I
authors.initials: I
authors.lastname: Gut
authors.forename: D
authors.initials: D
authors.lastname: Rocha
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D005787:Gene Frequency; D023281:Genomics; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide
keywords: Beef breed; cattle; linkage disequilibrium; single nucleotide polymorphism