On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young

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Fil: Bermann, Matías. University of Georgia. Department of Animal and Dairy Science. Athens, GA, USA.

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Autores principales: Bermann, Matías, Lourenco, Daniela, Forneris, Natalia Soledad, Legarra, Andrés, Misztal, Ignacy
Formato: Artículo publishedVersion
Lenguaje:Inglés
Publicado: 2022
Materias:
BIOLOGIA ANIMAL
GENETICA ANIMAL
GENOMICA FUNCIONAL
CIENCIAS BIOLOGICAS
Acceso en línea:http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2022bermann
Aporte de:
FAUBA Digital - Facultad de Agronomía (UBA) de Universidad de Buenos Aires
id snrd:2022bermann
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spelling snrd:2022bermann2026-03-26T10:27:42Z Bermann, Matías Lourenco, Daniela Forneris, Natalia Soledad Legarra, Andrés Misztal, Ignacy 2022 Fil: Bermann, Matías. University of Georgia. Department of Animal and Dairy Science. Athens, GA, USA. Fil: Lourenco, Daniela. University of Georgia. Department of Animal and Dairy Science. Athens, GA, USA. Fil: Forneris, Natalia Soledad. Universidad de Buenos Aires. Facultad de Agronomía. Buenos Aires, Argentina. Fil: Forneris, Natalia Soledad. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Instituto de Investigaciones en Producción Animal (INPA). Buenos Aires, Argentina. Fil: Legarra, Andrés. CONICET - Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Instituto de Investigaciones en Producción Animal (INPA). Buenos Aires, Argentina. Fil: Legarra, Andrés. GenPhySE. INRA. UMR. Castanet ‐ Tolosan, France. Fil: Misztal, Ignacy. University of Georgia. Department of Animal and Dairy Science. Athens, GA, USA. Background: Single - step genomic predictions obtained from a breeding value model require calculating the inverse of the genomic relationship matrix (G − 1. The Algorithm for Proven and Young (APY) creates a sparse representtion of G − 1 with a low computational cost. APY consists of selecting a group of core animals and expressing the breeding values of the remaining animals as a linear combination of those from the core animals plus an error term. The objectives of this study were to: (1) extend APY to marker effects models; (2) derive equations for marker effect estimates when APY is used for breeding value models, and (3) show the implication of selecting a specific group of core animals in terms of a marker effects model. Results: We derived a family of marker effects models called APY - SNP - BLUP. It differs from the classic marker effects model in that the row space of the genotype matrix is reduced and an error term is fitted for non - core animals. We derived formulas for marker effect estimates that take this error term in account. The prediction error variance (PEV) of the marker effect estimates depends on the PEV for core animals but not directly on the PEV of the non-core animals. We extended the APY-SNP-BLUP to include a residual polygenic effect and accommodate non-genotyped animals. We show that selecting a specific group of core animals is equivalent to select a subspace of the row space of the genotype matrix. As the number of core animals increases, subspaces corresponding to different sets of core animals tend to overlap, showing that random selection of core animals is algebraically justified. Conclusions: The APY-(ss)GBLUP models can be expressed in terms of marker effect models. When the number of core animals is equal to the rank of the genotype matrix, APY-SNP-BLUP is identical to the classic marker effects model. If the number of core animals is less than the rank of the genotype matrix, genotypes for non-core animals are imputed as a linear combination of the genotypes of the core animals. For estimating SNP effects, only relationships and estimated breeding values for core animals are needed. grafs. application/pdf 10.1186/s12711-022-00741-7 0999-193X (impreso) 1297-9686 (en linea) http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2022bermann eng info:eu-repo/semantics/openAccess openAccess openAccess http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4 Genetics Selection Evolution Vol.54 art.52 http://www.biomedcentral.com/ BIOLOGIA ANIMAL GENETICA ANIMAL GENOMICA FUNCIONAL CIENCIAS BIOLOGICAS On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young info:ar-repo/semantics/artículo info:eu-repo/semantics/article publishedVersion info:eu-repo/semantics/publishedVersion
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-140
collection FAUBA Digital - Facultad de Agronomía (UBA)
language Inglés
orig_language_str_mv eng
topic BIOLOGIA ANIMAL
GENETICA ANIMAL
GENOMICA FUNCIONAL
CIENCIAS BIOLOGICAS
spellingShingle BIOLOGIA ANIMAL
GENETICA ANIMAL
GENOMICA FUNCIONAL
CIENCIAS BIOLOGICAS
Bermann, Matías
Lourenco, Daniela
Forneris, Natalia Soledad
Legarra, Andrés
Misztal, Ignacy
On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
topic_facet BIOLOGIA ANIMAL
GENETICA ANIMAL
GENOMICA FUNCIONAL
CIENCIAS BIOLOGICAS
description Fil: Bermann, Matías. University of Georgia. Department of Animal and Dairy Science. Athens, GA, USA.
format Artículo
Artículo
publishedVersion
publishedVersion
author Bermann, Matías
Lourenco, Daniela
Forneris, Natalia Soledad
Legarra, Andrés
Misztal, Ignacy
author_facet Bermann, Matías
Lourenco, Daniela
Forneris, Natalia Soledad
Legarra, Andrés
Misztal, Ignacy
author_sort Bermann, Matías
title On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
title_short On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
title_full On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
title_fullStr On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
title_full_unstemmed On the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
title_sort on the equivalence between marker effect models and breeding value models and direct genomic values with the algorithm for proven and young
publishDate 2022
url http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2022bermann
work_keys_str_mv AT bermannmatias ontheequivalencebetweenmarkereffectmodelsandbreedingvaluemodelsanddirectgenomicvalueswiththealgorithmforprovenandyoung
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AT legarraandres ontheequivalencebetweenmarkereffectmodelsandbreedingvaluemodelsanddirectgenomicvalueswiththealgorithmforprovenandyoung
AT misztalignacy ontheequivalencebetweenmarkereffectmodelsandbreedingvaluemodelsanddirectgenomicvalueswiththealgorithmforprovenandyoung
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