Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

SIMPLE SUMMARY: Inbreeding depression is the decreased fitness of offspring of closely related individuals. It is a common problem in the livestock industry as a consequence of intense selection favoring few animals with higher genetic merit. The literature shows that inbred individuals may also exhibit decreased performance for economically relevant traits, such as growth in beef cattle. However, this relationship is not simple. The use of genetic markers can improve the detection of homozygous regions and improve the calculation of inbreeding coefficients. The working hypothesis of this study is that genomic homozygous regions can be used to predict animals’ performance. Moreover, homozygous regions across the genome differ in their effects. Our results indicate that the relationship between homozygosity and decreased performance varies by chromosome. Additionally, the inbreeding coefficient can be used to predict animals’ phenotype when calculated within a chromosome. This research warrants the development of a new approach in genomic selection to increase prediction accuracy by including information on homozygous regions. Additionally, management tools can be developed with the goal of breeding individuals with a purpose to decrease homozygosity only in the relevant regions of the genome. ABSTRACT: The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.