Abstract:

If the algorithm for proven and young (APY) is used to invert the genomic relationship matrix within the framework of Single-Step genomic evaluations, critical side-effects on genomic EBV can occur. Here we demonstrate that if parent animals are not included in the APY-core, their Mendelian sampling deviations are missing in the EBV of their offspring. Additionally, a critical downward bias in genomic predictions for some animals can occur under specific but not uncommon conditions. We illustrate some of the mechanisms involved using a small example and define the circumstances under which a downward bias will occur. Based on this definition, we selectively omit a small group of genotyped animals from the APYcore of the routine evaluation for protein yield in dual-purpose Fleckvieh to demonstrate the resulting effects on their Single-Step predictions.