AUTHOR=Kudinov Andrei A. , Koivula Minna , Aamand Gert P. , Strandén Ismo , Mäntysaari Esa A. 

TITLE=Single-step genomic BLUP with many metafounders

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1012205

DOI=10.3389/fgene.2022.1012205

ISSN=1664-8021

ABSTRACT=<p>Single-step genomic BLUP (ssGBLUP) model for routine genomic prediction of breeding values is developed intensively for many dairy cattle populations. Compatibility between the genomic (<bold>G</bold>) and the pedigree (<bold>A</bold>) relationship matrices remains an important challenge required in ssGBLUP. The compatibility relates to the amount of missing pedigree information. There are two prevailing approaches to account for the incomplete pedigree information: unknown parent groups (UPG) and metafounders (MF). unknown parent groups have been used routinely in pedigree-based evaluations to account for the differences in genetic level between groups of animals with missing parents. The MF approach is an extension of the UPG approach. The MF approach defines MF which are related pseudo-individuals. The MF approach needs a <bold>Γ</bold> matrix of the size number of MF to describe relationships between MF. The UPG and MF can be the same. However, the challenge in the MF approach is the estimation of <bold>Γ</bold> having many MF, typically needed in dairy cattle. In our study, we present an approach to fit the same amount of MF as UPG in ssGBLUP with Woodbury matrix identity (ssGTBLUP). We used 305-day milk, protein, and fat yield data from the DFS (Denmark, Finland, Sweden) Red Dairy cattle population. The pedigree had more than 6 million animals of which 207,475 were genotyped. We constructed the preliminary gamma matrix (<bold>Γ</bold><sub><italic>pre</italic></sub>) with 29 MF which was expanded to 148 MF by a covariance function (<bold>Γ</bold><sub>148</sub>). The quality of the extrapolation of the <bold>Γ</bold><sub><italic>pre</italic></sub> matrix was studied by comparing average off-diagonal elements between breed groups. On average relationships among MF in <inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi mathvariant="bold">Γ</mml:mi><mml:mn>148</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> were 1.8% higher than in <bold>Γ</bold><sub><italic>pre</italic></sub>. The use of <bold>Γ</bold><sub>148</sub> increased the correlation between the <bold>G</bold> and <bold>A</bold> matrices by 0.13 and 0.11 for the diagonal and off-diagonal elements, respectively. [G]EBV were predicted using the ssGTBLUP and Pedigree-BLUP models with the MF and UPG. The prediction reliabilities were slightly higher for the ssGTBLUP model using MF than UPG. The ssGBLUP MF model showed less overprediction compared to other models.</p>