# Comparison of linear and threshold models for genetic evaluation of morphological defects in Nellore cattle

## TL;DR

This study compares two genetic models to evaluate morphological defects in Nellore cattle, showing that both models give similar results and can help improve breeding.

## Contribution

The study introduces probability-scaled genomic estimated breeding values for morphological defects in cattle using large-scale data.

## Key findings

- Linear and threshold models produced similar heritability estimates for morphological defects in Nellore cattle.
- Genomic estimated breeding values from both models showed high correlation and consistent sire rankings.
- Depigmentation showed weak genetic correlations with other defects, suggesting distinct genetic control.

## Abstract

Morphological defects in beef cattle can compromise animal welfare and productivity, yet they remain underexplored in genetic evaluations. In this study, we assessed the prevalence and estimated genetic parameters for seven morphological defects in Nellore cattle, including depigmentation, feet and legs malformation, chamfer deviations, loin and jaw defects, hump irregularities, and navel abnormalities, using linear and threshold models. Data from over 180,000 animals recorded between 1998 and 2021 were analyzed. Defect prevalence increased over time, likely due to improved phenotyping and broader participation in data collection. After appropriate scale conversion, linear and threshold models yielded similar heritability estimates; with heritability ranging from 0.03 to 0.12 across traits. Genomic estimated breeding values from both models were expressed on the probability scale, with Spearman correlations of probability scaled values ranging from 0.89 to 0.94 across models. Agreement among commonly selected sires was also high (Spearman 0.94 to 0.97), indicating consistent rankings across models. Feet and legs malformations showed moderate positive correlations with chamfer (0.50) and jaw defects (0.51); chamfer had moderate correlated with hump (0.52); and loin had low positive correlated with jaw (0.34) and with feet and legs (0.39). Depigmentation showed weak correlations with all other traits (<0.20), suggesting distinct genetic control. These results support including morphological defects in routine genetic evaluations and underscore the value of model-appropriate transformations to maintain ranking consistency and interpretability.

This study provides the most comprehensive genetic evaluation of morphological defects in Nellore cattle to date, comparing linear and threshold models across over 180,000 animals. By introducing probability-scaled genomic estimated breeding values (GEBVs), it delivers actionable tools for reducing defect prevalence, improving animal welfare, and guiding breeding programs worldwide.