Metafounder approach for single-step genomic evaluations of Red Dairy cattle
Andrei A. Kudinov, Esa Mäntysaari, Gert Pedersen Aamand, Pekka Uimari, Ismo Strandén
Abstract
Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting genomic (G) and pedigree (A 22 ) relationship matrices complicate the implementation of ssGB-LUP into practice. The metafounder (MF) approach is a recently proposed solution for this problem and has been successfully used on simulated and real multibreed pig data. Advantages of the method are easily seen across breed evaluations, where pedigrees are traced to several pure breeds, which are thereafter used as MF. Application of the MF method to ruminants is complicated due to multi-breed pedigree structures and the inability to transmit existing unknown parent groups (UPG) to MF. In this study, we apply the MF approach for ssGBLUP evaluation of Finnish Red Dairy cattle treated as a single breed. Relationships among MF were accounted for by a (co)variance matrix () computed using estimated base population allele frequencies. The attained was used to calculate a relationship matrix A 22 for the genotyped animals. We tested the influence of SNP selection on the matrix by applying a minor allele frequency (MAF) threshold ( MAF ) where accepted markers had an MAF 0.05. Elements in the MAF matrix were slightly lower than in the matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A 22 ) to 0.76 (A 22 and