Controlling inbreeding in dairy cattle using genomic data

Inbreeding depression is the reduction in fitness in offspring resulting from mating individuals that share at least one common ancestor. The objective was to compare the effect of genome-wide and location specific homozygosity on fertility and milk production traits in dairy cattle. Pedigree inbreeding was compared with genomic inbreeding which is the realised proportion of the genome that is identical by descent (IBD). Genomic inbreeding can be used instead of pedigree inbreeding to estimate the effects of inbreeding depression and give similar estimates. A 1% increase in inbreeding reduces milk yield by around 20 litres per lactation and increases calving interval by around 0.2 days/year. Breeding programs could manage whole genome as well as site specific or targeted inbreeding, as homozygosity in regions of the genome that are sensitive to inbreeding (for milk production and fertility) could be avoided. Genomic regions were found that, when homozygous, have an effect on fertility by extending the calving interval by 5 to 12 days. The challenge is now to develop tools that can be used to control inbreeding using genomic information, such as mating plans.