Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP.
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).
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 |
format | article |
id | INIAOAI_09a99c130b6a9439ac06e0a145341d55 |
instacron_str | Instituto Nacional de Investigación Agropecuaria |
institution | Instituto Nacional de Investigación Agropecuaria |
instname_str | Instituto Nacional de Investigación Agropecuaria |
language | eng |
language_invalid_str_mv | en |
network_acronym_str | INIAOAI |
network_name_str | AINFO |
oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/2346 |
publishDate | 2022 |
reponame_str | AINFO |
repository.mail.fl_str_mv | lorrego@inia.org.uy |
repository.name.fl_str_mv | AINFO - Instituto Nacional de Investigación Agropecuaria |
repository_id_str | |
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 |