Swine

Interpretation of Genetic Values on the Probability Scale for Umbilical Hernia in a Swine Pure Line: Challenges in Defining Thresholds, Accuracy, and the Resistance Phenotype

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Abstract

Umbilical hernia in pigs represents a major challenge for the swine industry. Unlike pathogen-driven diseases where resilient animals can be infected without performance loss, umbilical hernia is a structural defect whose expression directly reduces animal value, even in otherwise healthy pigs. Identifying animals with the lowest genetic predisposition to express the defect, those with the lowest genetic risk, is essential for improving herd robustness. This study aimed to investigate the feasibility of the interpretation and validation of genetic values expressed on a probability scale for umbilical hernia in a pure line of pigs. Data from 637,000 animals from a pure line were analyzed. The phenotype was binary, coded as 1 (umbilical hernia present) or 2 (umbilical hernia absent). All animals with phenotypes were genotyped. Genetic 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 expressing umbilical hernia was computed using the PROBCATF90 software. For validation and interpretation, 1,769 sires with more than 100 progeny each were considered. A positive linear relationship was observed between sire probability-based EBVs and the proportion of affected progeny (r = 0.65). Probability intervals were then combined with progeny incidence to define practical threshold categories: >=30% (Low Risk), >=50% (Medium Risk), >=70% (Attention Risk), and >=90% (High Risk). Probability-scaled EBVs exhibited clear correspondence with observed defect incidence across categories. However, some sires with high probabilities showed low progeny incidence, likely reflecting environmental influences, differences in EBV accuracy, and maternal contributions. Sows may partially mitigate expression risk, as sires are typically mated to females of comparable genetic merit, though such patterns are difficult to control commercially. These findings underscore the importance of validating probability-scaled EBVs across environments and management systems. This framework allows a more intuitive interpretation of genetic risk and facilitates communication with producers by expressing results on a probability scale. Once validated, probability-scaled genetic values represent a promising framework for improving understanding of defect expression and supporting selection for robustness in swine populations. They allow the establishment of practical risk thresholds that guide selection and mating decisions, particularly when incidence is low or environments vary in control level. Continuous monitoring remains necessary to refine thresholds, ensure reliability across environments, and enhance applicability in commercial breeding programs.

Keywords: 2026

How to Cite:

Diaz, I., Borg, R., Bhatia, V., Walugembe, M., Rathje, T., Cross, A., Misztal, I., Lourenco, D. & Hidalgo, J., (2026) “Interpretation of Genetic Values on the Probability Scale for Umbilical Hernia in a Swine Pure Line: Challenges in Defining Thresholds, Accuracy, and the Resistance Phenotype”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286583. doi: https://doi.org/10.31274/wcgalp.24057

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