Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.

GARCÍA, A. - AGUILAR, I. - LEGARRA, A. - TSURUTA, S. - MISZTAL, I. - LOURENCO, D.

Resumen:

ABSTRACT. - BACKGROUND: Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large, for genotyped animals not in the official evaluations, and when interim evaluations are needed. Typically, IP are obtained for new batches of genotyped individuals, all of them young and without phenotypes. Individual (theoretical) accuracies for IP are rarely reported, but they are nevertheless of interest. Our first objective was to present equations to compute individual accuracy of IP, based on prediction error covariance (PEC) of SNP effects, and in turn, are obtained from PEC of GEBV in ssGBLUP. The second objective was to test the algorithm for proven and young (APY) in PEC computations. With large datasets, it is impossible to handle the full PEC matrix, thus the third objective was to examine the minimum number of genotyped animals needed in PEC computations to achieve IP accuracies that are equivalent to GEBV accuracies. © 2022. The Author(s).


Detalles Bibliográficos
2022
Algorithm
Breeding
Covariance
Prediction error
Single nucleotide polymorphism
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=63644&biblioteca=vazio&busca=63644&qFacets=63644
Acceso abierto
_version_ 1805580524216909824
author GARCÍA, A.
author2 AGUILAR, I.
LEGARRA, A.
TSURUTA, S.
MISZTAL, I.
LOURENCO, D.
author2_role author
author
author
author
author
author_facet GARCÍA, A.
AGUILAR, I.
LEGARRA, A.
TSURUTA, S.
MISZTAL, I.
LOURENCO, D.
author_role author
bitstream.checksum.fl_str_mv 4dd0877e2f905f555018bc02acdcb254
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2346/1/sword-2022-10-20T23%3a08%3a28.original.xml
collection AINFO
dc.creator.none.fl_str_mv GARCÍA, A.
AGUILAR, I.
LEGARRA, A.
TSURUTA, S.
MISZTAL, I.
LOURENCO, D.
dc.date.accessioned.none.fl_str_mv 2022-10-21T02:08:28Z
dc.date.available.none.fl_str_mv 2022-10-21T02:08:28Z
dc.date.issued.none.fl_str_mv 2022
dc.date.updated.none.fl_str_mv 2022-10-21T02:08:28Z
dc.description.abstract.none.fl_txt_mv ABSTRACT. - BACKGROUND: Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large, for genotyped animals not in the official evaluations, and when interim evaluations are needed. Typically, IP are obtained for new batches of genotyped individuals, all of them young and without phenotypes. Individual (theoretical) accuracies for IP are rarely reported, but they are nevertheless of interest. Our first objective was to present equations to compute individual accuracy of IP, based on prediction error covariance (PEC) of SNP effects, and in turn, are obtained from PEC of GEBV in ssGBLUP. The second objective was to test the algorithm for proven and young (APY) in PEC computations. With large datasets, it is impossible to handle the full PEC matrix, thus the third objective was to examine the minimum number of genotyped animals needed in PEC computations to achieve IP accuracies that are equivalent to GEBV accuracies. © 2022. The Author(s).
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=63644&biblioteca=vazio&busca=63644&qFacets=63644
dc.language.iso.none.fl_str_mv en
eng
dc.rights.es.fl_str_mv Acceso abierto
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:AINFO
instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv Algorithm
Breeding
Covariance
Prediction error
Single nucleotide polymorphism
dc.title.none.fl_str_mv Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
dc.type.none.fl_str_mv Article
PublishedVersion
info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description ABSTRACT. - BACKGROUND: Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large, for genotyped animals not in the official evaluations, and when interim evaluations are needed. Typically, IP are obtained for new batches of genotyped individuals, all of them young and without phenotypes. Individual (theoretical) accuracies for IP are rarely reported, but they are nevertheless of interest. Our first objective was to present equations to compute individual accuracy of IP, based on prediction error covariance (PEC) of SNP effects, and in turn, are obtained from PEC of GEBV in ssGBLUP. The second objective was to test the algorithm for proven and young (APY) in PEC computations. With large datasets, it is impossible to handle the full PEC matrix, thus the third objective was to examine the minimum number of genotyped animals needed in PEC computations to achieve IP accuracies that are equivalent to GEBV accuracies. © 2022. The Author(s).
eu_rights_str_mv openAccess
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repository.name.fl_str_mv AINFO - Instituto Nacional de Investigación Agropecuaria
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rights_invalid_str_mv Acceso abierto
spelling 2022-10-21T02:08:28Z2022-10-21T02:08:28Z20222022-10-21T02:08:28Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=63644&biblioteca=vazio&busca=63644&qFacets=63644ABSTRACT. - BACKGROUND: Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large, for genotyped animals not in the official evaluations, and when interim evaluations are needed. Typically, IP are obtained for new batches of genotyped individuals, all of them young and without phenotypes. Individual (theoretical) accuracies for IP are rarely reported, but they are nevertheless of interest. Our first objective was to present equations to compute individual accuracy of IP, based on prediction error covariance (PEC) of SNP effects, and in turn, are obtained from PEC of GEBV in ssGBLUP. The second objective was to test the algorithm for proven and young (APY) in PEC computations. With large datasets, it is impossible to handle the full PEC matrix, thus the third objective was to examine the minimum number of genotyped animals needed in PEC computations to achieve IP accuracies that are equivalent to GEBV accuracies. © 2022. The Author(s).https://hdl.handle.net/20.500.12381/2346enenginfo:eu-repo/semantics/openAccessAcceso abiertoAlgorithmBreedingCovariancePrediction errorSingle nucleotide polymorphismTheoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaGARCÍA, A.AGUILAR, I.LEGARRA, A.TSURUTA, S.MISZTAL, I.LOURENCO, D.SWORDsword-2022-10-20T23:08:28.original.xmlOriginal SWORD entry documentapplication/octet-stream2438https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2346/1/sword-2022-10-20T23%3a08%3a28.original.xml4dd0877e2f905f555018bc02acdcb254MD5120.500.12381/23462022-10-20 23:08:28.476oai:redi.anii.org.uy:20.500.12381/2346Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T02:08:28AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
GARCÍA, A.
Algorithm
Breeding
Covariance
Prediction error
Single nucleotide polymorphism
status_str publishedVersion
title Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
title_full Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
title_fullStr Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
title_full_unstemmed Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
title_short Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
title_sort Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
topic Algorithm
Breeding
Covariance
Prediction error
Single nucleotide polymorphism
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=63644&biblioteca=vazio&busca=63644&qFacets=63644