Quantitative and genomic analyses of inbreeding in dairy cattle populations

Abstract

The overall objective of this thesis was to assess the loss of genetic diversity, estimate the adverse effects of increasing homozygosity on economically important traits and investigate at the genomic level the unique location causing the detrimental effects. To understand the pattern of genetic diversity losses, we investigated the rate of inbreeding (∆F), rate of coancestry (∆f) and effective population size (N_e) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in Holstein and Jersey dairy cattle. The rate of inbreeding and coancestry were calculated using both the traditional pedigree method and genomic methods estimated from segment and marker-based approaches. The ∆F and ∆f per generation ranged from 0.62 to 1.16%. Therefore, the N_e ranged from 43 to 85 for the two breeds. This result suggests the need to implement measures and means for controlling the rate of inbreeding, which will help to manage and maintain farm animal genetic resources. Following the assessment of genetic diversity loss, the negative effects of the accumulation of inbreeding expected from the reducing N_e was investigated. More specifically, we investigated the effect of recent and ancient inbreeding on production and fertility traits in Holsteins. In general, negative effects of inbreeding were found on production and fertility traits with production traits having more significant negative effects. Interestingly, ancient inbreeding had no significant negative impact on traits analysed; however, recent inbreeding showed more adverse and significant impact on analysed traits. This result indicates that more attention should be focused on recent inbreeding. Furthermore, we sought to identify unique homozygous genomic regions (ROH) showing negative associations with production and fertility traits as well as investigating their effects. Unique ROH regions with unfavorable effects were identified for both production and fertility traits. These unique homozygous regions with negative effects on production and fertility traits were identified within and across multiple traits in almost all chromosomes. The identified harmful regions could be advantageously used in mate selection pipelines for minimizing their frequency in future generations.