Metafounders May Reduce Bias in Composite Cattle Genomic Predictions

Sabrina Kluska; Yutaka Masuda; José Bento Sterman Ferraz; Shogo Tsuruta; Joanir Pereira Eler; Fernando Baldi; Daniela Lourenco

doi:10.3389/fgene.2021.678587

Metafounders May Reduce Bias in Composite Cattle Genomic Predictions

Front Genet. 2021 Aug 20:12:678587. doi: 10.3389/fgene.2021.678587. eCollection 2021.

Authors

Sabrina Kluska^{1

2}, Yutaka Masuda², José Bento Sterman Ferraz³, Shogo Tsuruta², Joanir Pereira Eler³, Fernando Baldi¹, Daniela Lourenco²

Affiliations

¹ Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, Brazil.
² Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States.
³ Departamento de Medicina Veterinaìria, Universidade de São Paulo, Pirassununga, Brazil.

Abstract

Metafounders are pseudo-individuals that act as proxies for animals in base populations. When metafounders are used, individuals from different breeds can be related through pedigree, improving the compatibility between genomic and pedigree relationships. The aim of this study was to investigate the use of metafounders and unknown parent groups (UPGs) for the genomic evaluation of a composite beef cattle population. Phenotypes were available for scrotal circumference at 14 months of age (SC14), post weaning gain (PWG), weaning weight (WW), and birth weight (BW). The pedigree included 680,551 animals, of which 1,899 were genotyped for or imputed to around 30,000 single-nucleotide polymorphisms (SNPs). Evaluations were performed based on pedigree (BLUP), pedigree with UPGs (BLUP_UPG), pedigree with metafounders (BLUP_MF), single-step genomic BLUP (ssGBLUP), ssGBLUP with UPGs for genomic and pedigree relationship matrices (ssGBLUP_UPG) or only for the pedigree relationship matrix (ssGBLUP_UPGA), and ssGBLUP with metafounders (ssGBLUP_MF). Each evaluation considered either four or 10 groups that were assigned based on breed of founders and intermediate crosses. To evaluate model performance, we used a validation method based on linear regression statistics to obtain accuracy, stability, dispersion, and bias of (genomic) estimated breeding value [(G)EBV]. Overall, relationships within and among metafounders were stronger in the scenario with 10 metafounders. Accuracy was greater for models with genomic information than for BLUP. Also, the stability of (G)EBVs was greater when genomic information was taken into account. Overall, pedigree-based methods showed lower inflation/deflation (regression coefficients close to 1.0) for SC14, WWM, and BWD traits. The level of inflation/deflation for genomic models was small and trait-dependent. Compared with regular ssGBLUP, ssGBLUP_MF4 displayed regression coefficient closer to one SC14, PWG, WWM, and BWD. Genomic models with metafounders seemed to be slightly more stable than models with UPGs based on higher similarity of results with different numbers of groups. Further, metafounders can help to reduce bias in genomic evaluations of composite beef cattle populations without reducing the stability of GEBVs.

Keywords: Montana cattle; genomic selection; inflation; single-step genomic BLUP; unknown parent groups.