Single-step genomic evaluation for linear conformation and performance traits for German riding horses

Implementing systems for the estimation of genomic breeding values for horses is a major challenge, implying collaborative approaches for assembling a sufficiently large and informative reference population. In Germany, the collaboration of five horse breeding associations has enabled compiling a reference population with the focus on linear conformation and performance traits by the end of 2020. For the development of a prototype for genomic evaluation, the so-called single-step method was used, which allows including all available phenotypic, genotypic and pedigree data and thus maximizes the predictive value and reliability of the estimation. The genomic evaluation prototype has been validated using two approaches that provided consistent results: In the tenfold cross validation and in the forward validation, correlations between genomic breeding values (gEBVs) from the respective validation runs and the full run were moderate (0.6) to high (above 0.9). For most of the traits, correlations were in the higher range above 0.85, which, considering the available data, indicates a satisfactory stability of the developed system, but suggests some changes in the gEBVs in successive evaluation runs. Cross-validation revealed differences of results between the involved breeds that are regarded as minor. Use of the genotype data and estimation using the genomic relationship matrix resulted in more pronounced differentiation between individual horses, which may reflect a closer proximity of the gEBV to the true individual genetic predisposition. The benefit of including genomic information was illustrated for the cohort of linearly described horses born 2007-2017 which accounted for 98% of reference animals. In the genotyped horses, correlations between gEBVs from forward prediction and full run were higher (+0.03 to + 0.26) and standard deviations of gEBVs increased (> + 2.0) compared to the non-genotyped horses. In agreement with previous work on body size (withers height), this study did not reveal any findings which would interfere with performing single-step genomic evaluation for linear conformation and performance traits in German riding horses on the basis of a mixed reference population. Further calibrations are required to introduce it as a routine system in the near future.