PSXII-29 Partitioning of Inbreeding Depression using Pedigree and Genomic Approaches

Abstract

Abstract Understanding the accumulation of autozygosity over time in a genome could enhance the assessment of the effect of inbreeding and the mitigation of its harmful impact. To date, runs of homozygosity (ROH) have been commonly used to study inbreeding’s impact in livestock species, as an alternative to the pedigree-based approach. Although inbreeding caused by the mating of animals related through a recent common ancestor is reasonably expected to have more pronounced effects on traits, estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic information. Unfortunately, these methods are largely based on heuristic criteria (e.g., number of generations from common ancestor and length of ROH segments). To mitigate these deficiencies, we developed a method to classify inbreeding into recent and ancient classes based on a grid search driven by the hypothesis that new inbreeding tends to have a more pronounced effect than old inbreeding. The proposed method was tested using data from Line-1 Hereford cattle population characterized by a deep complete pedigree. Genomic data consisted of 50K SNP genotypes. Effect of recent and ancient inbreeding was assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes varied across traits and sources of information. Using pedigree information, increased inbreeding in the last 10 to 11 generations was considered as recent. When genomic information was using, thresholds ranged between 4 to 7 indicating the ability of ROH segments to better characterize the harmful impact of inbreeding in shorter periods of time. Using several model comparison criteria (adjusted R-squared, AIC, and BIC), the proposed method was better than existing approaches. Furthermore, the method provided a more objective quantitative approach for the classification of inbreeding.