Swine

Managing Genetic Risk of Umbilical Hernia in Swine Using Probability-Scaled Genetic Values in Different Management Environments.

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Abstract

Umbilical hernia is a structural anomaly adversely affects swine production. Phenotypically expressed as a binary disease trait (unaffected or affected), the incidence is highly dependent on environmental factors. However, selection based on genetic risk of umbilical hernia is possible. The challenge of estimating genetic risk within breeding populations is that incidence rates are low (below 4%) which reduces observable genetic variation and limits prediction accuracy. Furthermore, interpretation of breeding values is complex when the goal is to identify animals of low genetic risk across contrasting environments. The objective of this study was to validate estimated probability-scaled breeding values for umbilical hernia under two geographically different locations which represented distinctly different management environment where frequency of affected umbilical hernia pigs was either high (H = average of 10%) and low (L = average of 4%). Nucleus data from 637,000 pure line animals were analyzed. Breeding values were estimated using a threshold animal model implemented in the BLUPF90 suite of programs. The model included litter and contemporary group as random effects, and site, dam's total number born, sex and year, herd, and month as fixed effects. The probability of defect expression was computed using the PROBCATF90 software. For validation, 29 grandsires had progeny selected for breeding across two environments high (H) or low (L). Probability-based breeding values of grandsires ranged from 5% to 95% with higher percentage values represented higher genetic risk. High indexing offspring of grandsires were assigned for use as sires in either H or L locations. Progeny from sires in both locations were phenotyped. In the controlled environment (L), proportion of affected progeny ranged from 1% to 8%, whereas the less controlled environment (H) ranged from 1% to 20%, representing up to a 10% difference between progeny from equivalent probability-based breeding value sires. Discrepancies were more pronounced among high-risk sires, highlighting the substantial impact of environmental variation on phenotype observations. Dires with high-risk breeding values consistently had higher proportion of affected progeny under both environments. However, progeny from sires with probability-based breeding values >50% saw affected pigs ranging from 1%-5% and 8%-20% in L and H, respectively. Although breeding values rank sires consistently based on frequency of affected progeny across both environments, expression of affected individuals is much higher in H environment, reflecting a higher risk associated with sires of similar breeding values. Validation across environments supports the use of probability-scaled breeding values for selection. However, further research is needed to identify robust and generalizable cutoffs that accurately identify resilient animals under diverse production conditions to manage risk. Evaluating variation among individuals within the same probability class remains essential, and selection decisions should be tailored to both population and environment.

Keywords: 2026

How to Cite:

Borg, R., Diaz, I., Bhatia, V., Walugembe, M., Rathje, T., Cross, A., Misztal, I., Lourenco, D. & Hidalgo, J., (2026) “Managing Genetic Risk of Umbilical Hernia in Swine Using Probability-Scaled Genetic Values in Different Management Environments.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286618. doi: https://doi.org/10.31274/wcgalp.24069

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