PSVIII-24 Inbreeding levels of the Line 4 Hereford cattle population

Abstract Inbreeding is an increasing issue in the beef cattle industry due to increased use of artificial insemination (AI) and embryo transfer (ET). Inbreeding, or increased relatedness between animals, results in inbreeding depression and its effects have been well documented; reduced performance, reproduction, and profitability. However, there is a lack of understanding the molecular mechanisms involved in inbreeding depression. Long-term linebred populations offer a unique opportunity to better understand this, more specifically the Line 4 Hereford population. The population was established from the Line 1 Hereford population in 1962 and has been maintained by the Montana State University (MSU) Northern Agricultural Research Center (NARC) near Havre, MT since its establishment. Inbreeding was estimated using a complete pedigree (FPED) and genomic information on a subset of the population. A pedigree containing 3,453 animals was constructed covering years 1962 – 2018 and was used to calculate FCPED. Animals were selected for genotyping based on genetic contributions and availability. 241 semen, tissue, and blood samples were collected and genotyped with the Illumina Bovine GGP 50K BeadChip. Genomic inbreeding (FG) and pedigree inbreeding (FGPED) were evaluated for the 241 genotyped animals. Average rate of change in inbreeding per year was also evaluated. Runs of Homozygosity (ROH) analysis was performed in Golden Helix SVS v8.8.3. ROH were defined as a minimum run length of 500 kb with a minimum of 20 SNP. Inbreeding ranges were 0 – 34%, 0 – 98%, and 0 – 27% and the average inbreeding was 10.0%, 11.4%, and 15.3% for FPED, FG, and FGPED, respectively. The average rate of change in inbreeding per year was 0.3% over 57 years. Initial analysis found 30 regions identified by ROH, indicating that we can use ROH analysis and potentially Genome-Wide Association Studies (GWAS) to identify regions of the genome being impacted by inbreeding depression.