Estimation & Prediction

Meat EPDs: Marker-Effect Adjusted Technology to Improve Accuracy of Multi-Breed Derived EPDs for Young Animals

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Abstract

Multi-breed genetic evaluations benefit from sharing phenotypes and genotypes across participating populations. However, genomic predictions in these systems generally assume that SNP effects are homogeneous across breeds. Because linkage disequilibrium patterns and QTL-marker relationships differ among breeds, the magnitude and direction of marker effects also differ. Ignoring these differences may reduce the accuracy of predicted breeding values, particularly for young animals with limited phenotypic data. This study investigated whether breed-specific marker effects can be used to adjust multi-breed expected progeny differences (EPDs) and thereby improve accuracy and stability for young animals. Genotypes and multi-breed EPDs from more than 13,000 Limousin animals included in the July 2025 International Genetic Solutions (IGS) evaluation were used. Historical EPDs from April 2024 were available for 2,724 of these animals. A test population of 818 animals was selected based on exhibiting the largest changes in EPDs between the 2024 and 2025 evaluations. The remaining 12,415 animals were used to estimate Limousin-specific SNP effects for 47,343 markers using a BayesB model (π = 0.9) implemented in GenSel. Limousin molecular EPDs (MEPDs) were calculated from these breed-specific marker effects. Weighting coefficients for blending MEPDs with historical EPDs were derived from 1,906 non-test animals that possessed both historical and current EPDs but were not used in model training. These blended predictions are referred to as Marker-Effect Adjusted Technology (MEAT) EPDs. For the test population, MEAT EPDs consistently showed stronger agreement with the current IGS EPDs than historical EPDs. Correlations with current EPDs increased from 0.90 to 0.93 for calving ease, 0.88 to 0.96 for carcass weight, 0.92 to 0.96 for marbling, 0.90 to 0.96 for ribeye area, 0.90 to 0.97 for fat thickness, 0.95 to 0.98 for dry matter intake, and 0.79 to 0.93 for the $B2F index. In addition to higher accuracy, MEAT EPDs reduced the magnitude of year-to-year re-ranking. For example, the standard deviation of changes in the $B2F index decreased from 24 to 14 when MEAT EPDs were used in place of historical values. These results demonstrate that incorporating breed-specific SNP information can improve the accuracy and stability of multi-breed derived EPDs for young animals. The MEAT approach leverages existing genomic data without requiring changes to the multi-breed evaluation pipeline and may serve as a practical post-processing method for enhancing predictability in early-life animals. This methodology has potential value for seedstock producers, breed associations, and genetic evaluation programs aiming to minimize re-ranking and provide more reliable selection tools for commercial adoption.

Keywords: 2026

How to Cite:

Saatchi, M., (2026) “Meat EPDs: Marker-Effect Adjusted Technology to Improve Accuracy of Multi-Breed Derived EPDs for Young Animals”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286081. doi: https://doi.org/10.31274/wcgalp.23848

Rights: 1