This may be explained by the fact that only the phenotypically most extreme individuals are genotyped and only these are informative with respect to partitioning of residual and Mendelian sampling variances.
This is probably due to the selected study material, as only the most extreme families were genotyped, possibly reflecting the same phenomenon as seen in the study of Dong et al (2003).
The across family QTL for Trichostrongylus spp adults in the small intestine on chromosome 11 and the family 124 QTL for Trichostrongylus spp adults in the abomasum on chromosome 2 are both on chromosomes where only the most extreme animals were genotyped.
In the most extreme simulation, with 5% genotyping error, 5% missing data, 50% phenocopies, and 50% genetic heterogeneity, HFCC still had 71% power to detect some types of epistasis, although the power for other types of epistasis was smaller (34 51%).
In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped.
These animals are not necessarily the most phenotypic extremes for each trait but they are expected to be the most extreme with respect to the aggregated genotype, which is what we want to predict and genetically improve.
We did however concentrate on parasite burden as the primary trait of interest so that in choosing the most extreme animals for this trait for genotyping we were reducing our chances of finding QTL for the other traits examined.
For the analysis we compared the most extreme phenotypes, so compared allele and genotype frequencies between the best responders (ACR-Ped70 0r 70% improvement in joint count) and the worst responders (NR).
For a moderately heritable trait (h = 0.3), the increase in genetic gain with IBD-GS compared to classical pedigree-based selection was substantial, with relative increases of 23, 28, 31 and 32% by genotyping the phenotypic most extreme (top/bottom) 5, 10, 20%, and all training sibs, respectively.
