Metafounder approach for single-step genomic evaluations of Red Dairy cattle

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 (A₂₂) relationship matrices complicate the implementation of ssGBLUP into practice. The metafounder (MF) approach is a recently proposed solution for this problem and has been successfully used on simulated and real multi-breed 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 (Γ) computed using estimated base population allele frequencies. The attained Γ was used to calculate a relationship matrix A₂₂^Γ for the genotyped animals. We tested the influence of SNP selection on the Γ matrix by applying a minor allele frequency (MAF) threshold (Γ_MAF) where accepted markers had an MAF ≥0.05. Elements in the Γ_MAF matrix were slightly lower than in the Γ matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A₂₂) to 0.76 ( A₂₂^Γ and [Formula: see text] ). Average diagonal elements of A₂₂^Γ and [Formula: see text] matrices increased to the same level as in the G matrix. The ssGBLUP breeding values (GEBV) were solved using either the original 236 or redefined 8 UPG, or 8 MF computed with or without the MAF threshold. For bulls, the GEBV validation test results for the 8 UPG and 8 MF gave the same validation reliability (R²; 0.31) and over-dispersion (0.73, measured by regression coefficient b₁). No significant R² increase was observed in cows. Thus, the MF greatly influenced the pedigree relationship matrices but not the GEBV. Selection of SNP according to MAF had a notable effect on the Γ matrix and made the A₂₂ and G matrices more similar.