Genome‐wide linkage disequilibrium in the Blonde d'Aquitaine cattle breed. (17th August 2012) - Beghain, J.
Summary: 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.