Studies on rates of inbreeding and genetic diversity in Canadian dairy cattle

The purpose of this thesis was to monitor past and present, and to predict future rates of inbreeding and its consequence in remaining genetic diversity in Canadian dairy cattle, using real and simulated data. The detailed analyses of the pedigree of the Canadian Jersey and Holstein breeds showed an effective population size of about 60 and 120 for Jerseys and Holsteins, respectively. Genetic drift was identified as the most important cause of loss of genetic diversity in the two breeds, which reflects the accumulation of inbreeding and the small effective population size in both breeds. A study to determine if the additive genetic variance and heritability of economically important traits in Holsteins is declining over time was carried out. The Canadienne breed was used as an extreme case of a small population-sized breed to compare to Canadian registered Holsteins: For the Holsteins, the estimates of additive genetic variance showed a decreasing trend for all analyzed traits. The effect of accumulation of inbreeding on this decline was detected. For the Canadienne, additive genetic variance was found to be constant over time. The estimates of heritability over time showed a decreasing trend for the more intensively selected traits in both breeds. The decrease of additive genetic variance and heritability is an unfavorable trend as it may affect future response to selection for those traits. The possible implications of applying genomic selection in dairy cattle were investigated through simulation. Genomic selection resulted in lower inbreeding per generation and higher selection response than traditional selection. Additionally, minimum coancestry mating was found to be beneficial as it slowed down the accumulation of inbreeding in the population and made more genetic progress possible in the long term. The application of optimum contribution selection is also recommended to reduce true and pedigree estimated inbreeding, while keeping genetic progress at a desirable level. The possible strategies that would allow controlling future loss of genetic diversity in Canadian dairy breeds are discussed.