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The experimental design used for this study was based on large sire families, optimized for linkage analysis.
Using only maternally inherited haplotypes is a common practice in studies investigating LD with the sample population consisting of large sire half-sib families.
This relatively good accuracy of the sire model is probably specific to the dairy cattle situation where large sire families dominate the population structure.
DU: Duroc; LWF: Large White dam line; LWM: Large sire Male line; LR: Landrace; PI: Piétrain (XLSX 689 kb) Additional file 4: 70 pathways enriched to explain the biologically diversity of five pig breeds.
This would also promote the use of genomic predictions in other species for which sire models are less suited, because their family structures are less dominated by large sire families.
Nevertheless, given the magnitude of the estimated Ev for weight gain from birth to weaning and long-yearling weight, when model HET was fitted in the first step, a meaningful response to selection on EBV for residual variance of these traits would be expected in the case of large sire families.
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Pedigree 7 represented the genotyped Australian Holstein sires (courtesy of Australian Dairy Herd Improvement Scheme) comprising 20,792 individuals, across 13 generational tiers with the largest sire family size being 528 individuals.
Pedigree 6 was obtained from an Australian terminal sire sheep breed (courtesy of Sheep Genetics Australia) comprising 9,557 individuals across 21 generational tiers with the largest sire family size being 142 individuals.
Pedigree 8 was a human pedigree of genotyped individuals from the ORCADES study in the Orkney Islands, Scotland [ 17], comprising 12,294 individuals across 12 generational tiers with the largest sire family being 8 individuals.
Pedigree 5 was a real pedigree of a commercial pig population (courtesy of the Pig Improvement Company) comprising 6,242 individuals, across 16 generational tiers with the largest sire family size being 66 individuals.
Although assortative mating and associated maternal effects could be accounted for by identification of mothers, relationships in Fig. 1 may have been influenced by paternal, environmental effects (e.g. if greater parental care by larger sires accelerated development of larvae).
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