Genomic prediction and genome-wide association study for liver abscesses in crossbred beef cattle

Authors: Bradford, Heather; Kuehn, Larry; Snelling, Warren; Keel-Mercer, Brittney; Jones, Shuna; Thallman, Richard; Lindholm-Perry, Amanda

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2025
Publication Date: 9/5/2025
Citation: Bradford, H.L., Kuehn, L.A., Snelling, W.M., Keel, B.N., Jones, S., Thallman, R.M., Lindholm-Perry, A.K. 2025. Genomic prediction and genome-wide association study for liver abscesses in crossbred beef cattle. Journal of Animal Science. 103. Article skaf275. https://doi.org/10.1093/jas/skaf275.
DOI: https://doi.org/10.1093/jas/skaf275

Interpretive Summary: Liver abscesses cost the beef industry millions of dollars annually through reduced carcass weight and less efficient growth. Liver abscesses have been most often prevented by feeding prophylactic antibiotics. With pressure to reduce antibiotic use, other measures are needed to reduce liver abscess prevalence. Liver abscesses affect 10 to 20% of beef carcasses but can occur in 50% of individual lots. Genetic selection could be a permanent and cumulative approach to reducing liver abscesses. A large population of genotyped crossbred cattle was used to understand the genetics of liver abscesses. Based on this research, genetics have a very small contribution to the development of liver abscesses. The genomic heritability was near 0, suggesting little variation in liver abscesses was genetic. In addition, no candidate genes were identified as affecting liver abscess development. Because liver abscesses are primarily determined by environmental factors, management strategies will be more effective than genetic selection at reducing liver abscesses in beef cattle.

Technical Abstract: Liver abscesses are a concern in feedlot cattle, and little is known about the role of genetics in their development. This study aimed to estimate genetic parameters and to identify single nucleotide polymorphisms (SNP) associated with liver abscesses. Crossbred cattle representing 18 breeds in the United States Meat Animal Research Center Germplasm Evaluation Program were phenotyped for liver abscesses at slaughter (n = 9,044). Seventeen percent of cattle had liver abscesses. These cattle had genotypes that were imputed to sequence variant genotypes. After filtering and quality control, 340,723 SNP were used in the analysis. Liver abscess prevalence was modeled with a single-step genomic best linear unbiased prediction (ssGBLUP) threshold model using a Bayesian framework. The model included contemporary group (sex, treatment group, and slaughter date), additive genomic, and residual effects. Genomic heritability was 0.039 (95% highest posterior density = 0.005, 0.081), which was very small. To assess prediction quality, a 5-fold random cross-validation structure was used. Method Linear Regression was used to assess accuracy, bias, and dispersion by comparing estimated breeding values (EBV) from full and reduced analyses. Cross-validation metrics showed EBV based on genotypes had 0.05 reliability (SD < 0.01) with no bias relative to EBV based on genotypes and phenotypes. For the genome-wide association study, SNP effects were back calculated from the EBV solutions from ssGBLUP. No SNP were associated with liver abscesses at a Benjamini-Hochberg adjusted 0.05 significance level. Although a large dataset was used, this result was because of the low genomic heritability and imprecise EBV used to calculate SNP effects. Based on these results, environmental factors contribute to most of the variation in liver abscesses. Genetic selection to reduce liver abscesses would be slow because of the low genomic heritability, measurement late in life, and inability to measure breeding animals. A faster approach would be finding additional environmental interventions that maintain animal performance.