Technical note: Genetic groups in single-step single nucleotide polymorphism best linear unbiased predictor

Abstract

Genetic groups, also called unknown or phantom parents groups, are often used in dairy cattle genetic evaluations to account for selection that cannot be accounted for by known genetic relationships. With the advent of genomic evaluations, the theory of genetic groups was extended to the so-called single-step genomic BLUP (ssGBLUP). In short, genetic groups can be fitted in ssGBLUP through regression effects, or by including them in the pedigree and computing the adequate combined pedigree and genomic relationship matrix. In this study, we applied the so-called Quaas and Pollak transformation to a system of equations for single-step SNP BLUP (ssSNPBLUP), such that genetic groups can thereafter be included in the pedigree. The example in this study showed that including the genetic groups in the pedigree for ssSNPBLUP allowed reduced memory burden and computational costs in comparison to genetic groups fitted as covariates.