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Reliabilities of estimated breeding values in models with metafounders

Genetics selection evolution (Paris), 2023-01, Vol.55 (1), p.6-6, Article 6 [Peer Reviewed Journal]

2023. The Author(s). ;COPYRIGHT 2023 BioMed Central Ltd. ;The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Attribution ;The Author(s) 2023 ;ISSN: 1297-9686 ;ISSN: 0999-193X ;EISSN: 1297-9686 ;DOI: 10.1186/s12711-023-00778-2 ;PMID: 36690938

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  • Title:
    Reliabilities of estimated breeding values in models with metafounders
  • Author: Bermann, Matias ; Aguilar, Ignacio ; Lourenco, Daniela ; Misztal, Ignacy ; Legarra, Andres
  • Subjects: Analysis ; Animal genetics ; Animals ; Biotechnology ; Breeding ; Computer Science ; Environmental Sciences ; Genetic relationship ; Genetics ; Genome ; Genomics - methods ; Genotype ; Heterozygosity ; Life Sciences ; Male ; Modeling and Simulation ; Models, Genetic ; Nucleotides ; Pedigree ; Phenotype ; Phenotypes ; Polymorphism ; Populations ; Predictions ; Progeny ; Quantitative genetics ; Reliability ; Reliability analysis ; Reproducibility of Results ; Risk assessment ; Sheep ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism
  • Is Part Of: Genetics selection evolution (Paris), 2023-01, Vol.55 (1), p.6-6, Article 6
  • Description: Reliabilities of best linear unbiased predictions (BLUP) of breeding values are defined as the squared correlation between true and estimated breeding values and are helpful in assessing risk and genetic gain. Reliabilities can be computed from the prediction error variances for models with a single base population but are undefined for models that include several base populations and when unknown parent groups are modeled as fixed effects. In such a case, the use of metafounders in principle enables reliabilities to be derived. We propose to compute the reliability of the contrast of an individual's estimated breeding value with that of a metafounder based on the prediction error variances of the individual and the metafounder, their prediction error covariance, and their genetic relationship. Computation of the required terms demands only little extra work once the sparse inverse of the mixed model equations is obtained, or they can be approximated. This also allows the reliabilities of the metafounders to be obtained. We studied the reliabilities for both BLUP and single-step genomic BLUP (ssGBLUP), using several definitions of reliability in a large dataset with 1,961,687 dairy sheep and rams, most of which had phenotypes and among which 27,000 rams were genotyped with a 50K single nucleotide polymorphism (SNP) chip. There were 23 metafounders with progeny sizes between 100,000 and 2000 individuals. In models with metafounders, directly using the prediction error variance instead of the contrast with a metafounder leads to artificially low reliabilities because they refer to a population with maximum heterozygosity. When only one metafounder is fitted in the model, the reliability of the contrast is shown to be equivalent to the reliability of the individual in a model without metafounders. When there are several metafounders in the model, using a contrast with the oldest metafounder yields reliabilities that are on a meaningful scale and very close to reliabilities obtained from models without metafounders. The reliabilities using contrasts with ssGBLUP also resulted in meaningful values. This work provides a general method to obtain reliabilities for both BLUP and ssGBLUP when several base populations are included through metafounders.
  • Publisher: France: BioMed Central Ltd
  • Language: English;German
  • Identifier: ISSN: 1297-9686
    ISSN: 0999-193X
    EISSN: 1297-9686
    DOI: 10.1186/s12711-023-00778-2
    PMID: 36690938
  • Source: Hyper Article en Ligne (HAL) (Open Access)
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