Using a family-based structure to detect the effects of genomic inbreeding on embryo viability in Holstein cattle

摘要

Recent evidence has suggested that some of the decline in reproductive ability in dairy cattle has been caused by embryonic death. The current study compared expected genomic inbreeding from sire-dam mating pairs to genomic inbreeding from live progeny in an attempt to determine how embryonic inbreeding may affect fertility. A total of 11,484 Holstein cattle with 43,485 SNP markers and pedigree information were available for analysis. A total of 412 sire-dam-progeny trios in which all animals had reliable genotypes were discovered. After removal of trios because of parentage errors, 374 remained for analysis. Additionally, a total of 3,031 animals comprising 3,906 genotyped full-sibling pairs were available for comparison. Expected genomic inbreeding measures were calculated by predicting ho-mozygosity independently per SNP (F_(PHE)) in sire-dam mating pairs and by simulating progeny using phased haplotype information (F_(ROHE) and F_(PHE)). Actual genomic inbreeding measures were calculated using the percent homozygosity of all SNP (F_(PH)) and using runs of homozygosity (F_(ROH)). Average F_(PHE) values (62.8 ± 0.78%) were slightly lower than F_(PH) (63.1 ± 1.12%), when considering each SNP independently. After phasing haplotypes, F_(PHE) (62.5 ± 0.83%) was again slightly lower than F_(PH) (62.7 ± 1.16%), and F_(ROHE) (3.46 ± 1.54%) was slightly lower than F_(ROH) (3.53 ± 2.17%). Results suggest increases in expected genomic inbreeding do not explain a large effect on embryo viability at average levels of expected inbreeding. Higher variation in F_(ROH) values was present with sire-dam mating pairs exhibiting high F_(ROHE), which may suggest high levels of genomic inbreeding are required for a noticeable effect on overall embryo viability. Genomic inbreeding between full siblings was also compared with moderate correlations (0.47-0.52) present. Overall, expected genomic inbreeding measures were calculated, but results did not suggest a large effect of expected inbreeding on embryo viability.