Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s12859-016-1439-1 http://hdl.handle.net/11449/159301 |
Resumo: | Background: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far. Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP. Moreover, we discuss an alternative categorical epistasis model (CE) eliminating undesired properties of EGBLUP and show that the CE model can improve predictive ability. Finally, we demonstrate that the coding-dependent performance of EGBLUP offers the possibility to incorporate prior experimental information into the prediction method by adapting the coding to already available phenotypic records on other traits. Conclusion: Based on our results, for EGBLUP, a symmetric coding {-1, 1} or {-1, 0, 1} should be preferred, whereas a standardization using allele frequencies should be avoided. Moreover, CE can be a valuable alternative since it does not possess the undesired theoretical properties of EGBLUP. However, which model performs best will depend on characteristics of the data and available prior information. Data from previous experiments can for instance be incorporated into the marker coding of EGBLUP. |
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Repositório Institucional da UNESP |
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2946 |
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Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)Genomic predictionEpistasis modelInteractionBackground: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far. Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP. Moreover, we discuss an alternative categorical epistasis model (CE) eliminating undesired properties of EGBLUP and show that the CE model can improve predictive ability. Finally, we demonstrate that the coding-dependent performance of EGBLUP offers the possibility to incorporate prior experimental information into the prediction method by adapting the coding to already available phenotypic records on other traits. Conclusion: Based on our results, for EGBLUP, a symmetric coding {-1, 1} or {-1, 0, 1} should be preferred, whereas a standardization using allele frequencies should be avoided. Moreover, CE can be a valuable alternative since it does not possess the undesired theoretical properties of EGBLUP. However, which model performs best will depend on characteristics of the data and available prior information. Data from previous experiments can for instance be incorporated into the marker coding of EGBLUP.Open Access Publication Funds of the Gottingen UniversityKWS SAAT SEChina Scholarship Council (CSC)grants FONCyTUBACyTPIP CONICET, from ArgentinaGeorg August Univ, Dept Anim Sci, Albrecht Thaer Weg 3, Gottingen, GermanySouth China Agr Univ, Natl Engn Res Ctr Breeding Swine Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Coll Anim Sci, Guangzhou, Guangdong, Peoples R ChinaSao Paulo State Univ, Dept Zootecnia, Sao Paulo, BrazilKWS SAAT SE, Einbeck, GermanyBavarian State Res Ctr Agr, Inst Anim Breeding, Grub, GermanyUniv Buenos Aires, INPA CONICET, Dept Anim Prod, Buenos Aires, DF, ArgentinaSao Paulo State Univ, Dept Zootecnia, Sao Paulo, Brazilgrants FONCyT: PICT 2013-1661UBACyT: 20020150100230B/2016PIP CONICET, from Argentina: 833/2013Biomed Central LtdGeorg August UnivSouth China Agr UnivUniversidade Estadual Paulista (Unesp)KWS SAAT SEBavarian State Res Ctr AgrUniv Buenos AiresMartini, Johannes W. R.Gao, NingCardoso, Diercles F. [UNESP]Wimmer, ValentinErbe, MalenaCantet, Rodolfo J. C.Simianer, Henner2018-11-26T15:37:51Z2018-11-26T15:37:51Z2017-01-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article16application/pdfhttp://dx.doi.org/10.1186/s12859-016-1439-1Bmc Bioinformatics. London: Biomed Central Ltd, v. 18, 16 p., 2017.1471-2105http://hdl.handle.net/11449/15930110.1186/s12859-016-1439-1WOS:000392147900003WOS000392147900003.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBmc Bioinformatics1,479info:eu-repo/semantics/openAccess2023-11-01T06:10:52Zoai:repositorio.unesp.br:11449/159301Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-11-01T06:10:52Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
title |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
spellingShingle |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) Martini, Johannes W. R. Genomic prediction Epistasis model Interaction |
title_short |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
title_full |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
title_fullStr |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
title_full_unstemmed |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
title_sort |
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
author |
Martini, Johannes W. R. |
author_facet |
Martini, Johannes W. R. Gao, Ning Cardoso, Diercles F. [UNESP] Wimmer, Valentin Erbe, Malena Cantet, Rodolfo J. C. Simianer, Henner |
author_role |
author |
author2 |
Gao, Ning Cardoso, Diercles F. [UNESP] Wimmer, Valentin Erbe, Malena Cantet, Rodolfo J. C. Simianer, Henner |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Georg August Univ South China Agr Univ Universidade Estadual Paulista (Unesp) KWS SAAT SE Bavarian State Res Ctr Agr Univ Buenos Aires |
dc.contributor.author.fl_str_mv |
Martini, Johannes W. R. Gao, Ning Cardoso, Diercles F. [UNESP] Wimmer, Valentin Erbe, Malena Cantet, Rodolfo J. C. Simianer, Henner |
dc.subject.por.fl_str_mv |
Genomic prediction Epistasis model Interaction |
topic |
Genomic prediction Epistasis model Interaction |
description |
Background: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far. Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP. Moreover, we discuss an alternative categorical epistasis model (CE) eliminating undesired properties of EGBLUP and show that the CE model can improve predictive ability. Finally, we demonstrate that the coding-dependent performance of EGBLUP offers the possibility to incorporate prior experimental information into the prediction method by adapting the coding to already available phenotypic records on other traits. Conclusion: Based on our results, for EGBLUP, a symmetric coding {-1, 1} or {-1, 0, 1} should be preferred, whereas a standardization using allele frequencies should be avoided. Moreover, CE can be a valuable alternative since it does not possess the undesired theoretical properties of EGBLUP. However, which model performs best will depend on characteristics of the data and available prior information. Data from previous experiments can for instance be incorporated into the marker coding of EGBLUP. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-01-03 2018-11-26T15:37:51Z 2018-11-26T15:37:51Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/s12859-016-1439-1 Bmc Bioinformatics. London: Biomed Central Ltd, v. 18, 16 p., 2017. 1471-2105 http://hdl.handle.net/11449/159301 10.1186/s12859-016-1439-1 WOS:000392147900003 WOS000392147900003.pdf |
url |
http://dx.doi.org/10.1186/s12859-016-1439-1 http://hdl.handle.net/11449/159301 |
identifier_str_mv |
Bmc Bioinformatics. London: Biomed Central Ltd, v. 18, 16 p., 2017. 1471-2105 10.1186/s12859-016-1439-1 WOS:000392147900003 WOS000392147900003.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bmc Bioinformatics 1,479 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
16 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd |
publisher.none.fl_str_mv |
Biomed Central Ltd |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803046266306822144 |