When the breed studied has a reduced intra-breed diversity, the combination of dogs from international locations does not increase the rate of false positives and potentially increases the power of association studies.
The clinical phenotype of BSE in the genotypes and breed studied was indistinguishable from that described for classical scrapie cases.
As expected from SNP and sequence data [ 1, 3], Boxers were the least diverse breed studied and Border Collies were the most diverse breed (Table 3).
All were purebred: French bulldogs were the commonest breed studied and accounted for 29 of the 50 cases (58%), while other breeds evaluated included English bulldogs (n = 8, 16%), Pug (n = 12, 24%) and Shih-tzu (n = 1, 2%).
Of interest, a subset of the EASZ calves has European taurine ancestry, while the other East African cattle breed studied, the Sheko, shows no European taurine introgression (Supplementary Table S1).
Comparisons in this multi-breed study were not adjusted for potential confounders, and clustering of deafness within litter was not accounted for.
One branch, which was composed of the Abondance, Montbéliarde and Tarentaise breeds, was taken as an example of closely related breeds and these breeds were merged for the multi-breed study.
Genetic differentiation within the ESM, MLB and AR breeds, respectively 0.17, 0.11 and 0.10, was higher than those obtained by Berthouly et al.[ 9] and Serrano et al.[ 8] in their intra-breed study of the genetic diversity of goat populations, but the number of common markers is smaller (Table 6).
Gautier et al. [ 43] reported the LD analysis of 526 SNPs mostly located on one chromosome in 14 breeds and suggested a common panel of 300,000 SNPs (one SNP every 10 kb) for association mapping in different breeds similar to the requirement for a high power panel within-breed study as shown here.
