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This means that for predictions based on intermediate marker density (50 k) and GBLUP, it is currently necessary to use breed-specific reference populations.
The intra-provenance variation observed suggests that admixtures from different provenances should not be used (Breed et al. 2013), when sourcing seeds for restoration.
Combined analysis of all four breeds was performed using breed as strata.
Using breed-specific allele frequencies is expected to give different results (e.g., [ 20]).
Hence, using breed-specific allele frequencies in constructing the GRM had a limited impact on prediction accuracy.
This was previously shown in beef breeds where using breeds with smaller sample sizes reduced the power to identify segregating loci [ 18].
Here, the Wei and van der Werf [ 1] model is reformulated using breed-specific partial relationship matrices, as in Garcia-Cortes and Toro [ 20].
However, the growth rate gains with antibiotic growth promotants are less significant with currently used breeds of swine and poultry (Wegener 2003).
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.
Although some people feel that a wide range of dog breeds can be raised to protect livestock, the most commonly used breeds include: Akbash.
We estimated genome-wide significance using the breed permutation procedure used in ref. [ 12].
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