The overall differences in allele frequency among breeds also caused general inflation of association P-values, complicating the interpretation.
One would therefore expect that some of the loci associated with these traits should show strong differences in genotype frequency between breeds, which would show up in a calculation of FST.
Overall, these results indicate that the accuracy of across-breed genomic prediction is small because of differences in LD, e.g. [ 7, 11], absence of family relationships, e.g. [ 13, 49], and differences in allele frequency across breeds, e.g. [ 2]; in addition, all these factors are probably entangled with each other.
Recently, Makgahlela et al. [ 14] compared predictions using a genomic relationship matrix based on average allele frequencies across breeds with predictions using breed-specific allele frequencies in the Nordic Red dairy cattle population.
The average F ST was calculated in each 250 kb window following Weir & Cockerham [ 66] as: 1 where j is each SNP in the 250 kb window, p ij is the allele frequency for breed i at SNP j, and is the mean allele frequency of the breeds at SNP j.
In the second method (G2), the GRM was calculated based on haplotypes and using allele frequencies that pertain to the breed of each parental haplotype, to take into account different marker allele frequencies between breeds in crossbred data.
Specifically, with dominance, the QTL allele substitution effect for breed A on performance of AxB crossbreds is equal to a+d 1-2pB), where pB is the QTL allele frequency in breed B and a and d are the additive and dominance effects at the QTL [ 19].
Frequency has bred cynicism, mostly because these convincing apologies are so often preceded by equally convincing denials of any wrongdoing.
These recently described alternatives for SNP selection take different marker allele frequencies between breeds and crossbred data into account.
Thus, differences in allele frequencies between breeds, along with dominant gene action, can be attributed to the low accuracy of prediction across breeds in dairy cattle.
