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.
Highlights
Single-step genomic BLUP has been widely used for genomic evaluation in domestic species such as dairy and beef cattle, swine, and chicken (Chen et al, 2011; Tsuruta et al, 2013; Lourenco et al, 2015b; Song et al, 2017)
Traits included scrotal circumference at 14 months of age (SC14, cm), post weaning weight gain (PWG, kg; calculated as the difference between yearling weight adjusted to 420 days of age and weaning weight adjusted to 205 days of age), weaning weight (WW, kg; weaning weight adjusted to 205 days of age), and birth weight (BW, kg)
unknown parent groups (UPGs) solutions from models where UPGs were only taken into account in A matrices were higher than those from models with UPGs in all relationship matrices
Summary
Single-step genomic BLUP (ssGBLUP) has been widely used for genomic evaluation in domestic species such as dairy and beef cattle, swine, and chicken (Chen et al, 2011; Tsuruta et al, 2013; Lourenco et al, 2015b; Song et al, 2017). The realized relationship matrix (H) used in ssGBLUP was developed under assumptions that may not hold in practice and may result in biased genomic estimated breeding value (GEBV), especially when pedigree information is missing for genotyped animals (Misztal et al, 2013). In such a case, incompatibilities between the genomic (G) and pedigree (A) relationship matrices are observed (Misztal et al, 2013). Several approaches have been proposed to solve the incompatibility between G and A in ssGBLUP, namely, truncation of pedigree to the most recent generations (Lourenco et al, 2014), scaling parameters for G and A (Aguilar et al, 2010), and different ways to construct G (Chen et al, 2011; Simeone et al, 2012)
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