SNPs in the region surrounding the ABCG2 locus [ 14] on BTA6 showed a much stronger signal in Holstein within breed analysis than the multibreed analysis, as there was no evidence that this mutation was segregating in our Jersey population.
The recessive white mutation is segregating in a chicken line maintained at the INRA experimental farm 'UE-GFA' located in Nouzilly, near Tours.
Author response: Bulmer's model assumes that the fate of a new mutation is decided independently of other mutations, that is to say that generally only one mutation is segregating in the population at the same time.
For example, if a single causative mutation is segregating in an F2 population, our model predicts that the power of BSA-seq to detect a mutation changing the phenotype by 5% relative to wild type is greater than 0.9 for a total population size of 10, a 5% cutoff for phenotypic selection, and an average sequencing coverage of 25×.
Further, the optimal level of DC may be above 2-fold if hypomorphic mutations are segregating.
We caution, however, that it is not clear to what extent premature stops or frameshift mutations are segregating in these species or are the outcome of sequencing errors.
If AT mutations are segregating at higher frequency due to alignment errors, we would expect the pattern to be stronger in noncoding than coding regions.
We would expect that, in data in which more causal mutations are segregating and with many more animals, estimates of Pr would be less sensitive to the prior.
If the selected mutations were segregating on multiple different haplotypes before selection began, the iHS statistic may have too little power to detect the selection signature.
In cluster 1, both non-synonymous and synonymous mutations were segregating at lower frequencies than would be predicted under strict neutrality.
