Reconstructing the Genetic History of Cattle and the Potential Impact on Future Genetic Gains in the Beef and Dairy Industries

The genetic gain that is possible from genomic selection depends on the intensity of selection, the generation interval, the genetic variation that exists for the trait, and the extent of linkage disequilibrium between genetic markers and the mutations affecting the trait. The latter two parameters are highly dependent on the ancestral demography of the population, particularly the change in effective population size over time. Whole-genome sequence is a rich source of genetic data for inferring these changes. Here we use sequencesfrom key Holstein ancestor bulls to infer stepwise changes in ancestral demography for cattle up to the present. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago. This is followed by a further reduction coinciding with cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. The large ancestral Ne explains the high rate of polymorphism that is observed in cattle sequence data. Next we use this inferred demography to inform a simulation of genomic selection in a dairy or beef cattle population, using either 50K, 800K or full sequence data. The results indicate that combining multiple breeds in the training population will potentially maximise the advantage of sequence data, particularly in achieving improved persistence of accuracy in genomic breeding values over generations.