Lazy computation of Residual Polygenic effects

Abstract

Single step methods use a blended relationship matrix that contains a fraction (typically 5%-20%) of pedigree-based relationships, called Residual Polygenic Effect (RPG). Indirect predictions of animals not included in the Mixed Model Equations (MME) are composed by a Direct Estimated Genomic Value (DGV), a sum of SNP readings times their solutions, and an RPG. Computation of RPG is not straightforward, and involves some complicated algebra and software, including separate relationships for genotyped and non-genotyped animals. We propose an alternative, equivalent computation that infers RPG for genotyped animals in the MME as RPG=GEBV-DGV, and then solves BLUP equations with RPG as “record” with heritability close to 1. The solution is the RPG for all animals in the MME, from which Parent Average can be used for Indirect Predictions. We show feasibility in practice with a US data set with millions of animals genotyped and in pedigree.