Meta-model for genomic relationships of metafounders applied on large scale single-step random regression test-day model
In this study traditional genetic groups and metafounders were compared in analysis of a random regression TD model with ssGTBLUP. The compared models were 1) ssGTBLUP with QP transformation of genetic groups and a genomic relationship matrix G built using base population allele frequencies for the markers, 2) ssGTBLUP with QP transformation of genetic groups and G with the same allele frequency of 0.5 for the markers, 3) ssGTBLUP with the metafounder (MF) approach and G with the same allele frequency 0.5. All models used VanRaden method 1 in G and had a 30% residual polygenic proportion (RPG). The G matrix in cases 1) and 2) was scaled to have average diagonal equal to the pedigree-based relationship matrix A22 of genotyped animals. Models 2) and 3) gave very similar results in terms of overprediction. Also, it seems that ssGTBLUP is quite robust to allele frequency used in the G matrix. However, the MF approach might be more efficient in reducing bias. In conclusion, both the QP transformation and the MF approach can be implemented in large-scale ssGTBLUP evaluation.
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