Genomic validation software: USA update including truncated MACE

Abstract

With the need to establish a standardized method to validate genomic estimated breeding values (GEBV) to meet the requirements for marketing the semen of young bulls in Europe, the Interbull Centre has routinely added new features to the GEBVtest software. In 2023, the United States (US) conducted a GEBV validation and reported that large population breeds and traits with high heritability were more stable, whereas smaller populations and complex traits often failed due to various reasons. In addition, the use of Truncated MACE (TMACE)-based genomic evaluations was recommended to verify if this model would outperform 4-year-old official results. A new version of the GEBVtest software will become the standard for GEBV validation in 2024. The new version includes bootstrapping to improve and expand significance, with better tests for slopes, validation accuracy, and bias and does not allow bulls with GEBV foreign proof to be included as candidates. In this study, GEBV validation was performed using the newest version of the GEBVtest software while validating truncated domestic plus TMACE instead of using official US predictions from 4 years ago and applied to US dairy cattle populations. Nine traits were tested and GEBV from August 2023 were used as the full dataset, whereas TMACE-based GEBV were used as the truncated dataset. A TMACE-based model can accommodate model or data changes over time as well as a validation on traits that were not even implemented four years ago such as mastitis for more breeds implemented in 2020 and 2022 in the US. In general, the inclusion of TMACE improved results for all breeds. For Holstein, all traits passed validation except for one trait that failed with a slope (b₁) of 1.31 (>1.2). The b₁ standard error was 0.02, which confirms an underestimation of this trait. In smaller breeds, a few other traits failed validation due to a b₁ < 0.8, but showed clear improvement of the b₁ by including TMACE. Finally, the smallest breeds showed several inconclusive passes and fewer failures compared to a previous study. The results may be due to the complexity of traits and the small number of candidate bulls. The use of TMACE-based genomic evaluations improves the validation test and is a tool to be considered as standard when performing GEBV validation, especially for smaller breeds.