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Abstract
Assessment of individual inbreeding and its effects are traditionally based on pedigree information. Pedigree-based estimates of inbreeding suffer from the limitations in the availability, quality and completeness of genealogical information. Genomic information provided an unprecedented opportunity for the direct assessment of inbreeding. Runs of homozygosity (ROH) have been recognized as hallmarks of inbreeding. Inbreeding based on ROH segments (F_ROH) allows for the direct estimation of the realized autozygosity as well as its age-related components (ancient and recent inbreeding). Furthermore, ROH segments can be used to estimate inbreeding and its effects at the chromosome, genome segment, or SNP levels. Yearling weight and ADG were significantly affected by inbreeding in beef cattle. However, little to no inbreeding depression was observed for birth and weaning weights. ROH based estimates of inbreeding still suffer from several shortcomings. Chief among them is the subjective setting of the minimum threshold to declare an autozygous tract as an ROH segment. Using knowledge of deleterious mutation’s enrichment in ROH, a method to approximate the minimum ROH length was developed using phenotypic information. The estimated thresholds were trait-specific and had the ability to capture inbreeding depression at its onset. The characterization and the classification of inbreeding into age classes is very useful for a better understanding of the rise and purging of deleterious autozygosity and for the optimization of inbreeding management schemes. Use of subjective thresholds to discriminate between recent and ancient inbreeding, as it is currently the case, biases the estimation of inbreeding depression. The lengths of ROH segments are correlated with the age of inbreeding. Long segments reflect a more recent inbreeding. We developed a grid search-based approach to classify inbreeding into age classes using ROH segments and pedigree information guided by the well supported hypothesis that new inbreeding is more harmful than the old one. Using ROH segments, recent inbreeding was estimated to occur with the last 4 to 7 generations for the different traits compared to 10 to 11 generations using pedigree information. The thresholds separating old and new inbreeding were trait-specific and better characterized inbreeding depression compared to thresholds derived from existing methods.