Genomic prediction with epistasis models: On the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)
- Autores
- Martini, Johannes W. R.; Gao, Ning; Cardoso, Diercles F.; Wimmer, Valentin; Erbe, Malena; Cantet, Rodolfo Juan Carlos; Simianer, Henner
- Año de publicación
- 2017
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- 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.
Fil: Martini, Johannes W. R.. Georg-August University; Alemania
Fil: Gao, Ning. Georg-August University; Alemania
Fil: Cardoso, Diercles F.. Georg-August University; Alemania
Fil: Wimmer, Valentin. KWS SAAT SE; Alemania
Fil: Erbe, Malena. Georg-August University; Alemania
Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina
Fil: Simianer, Henner. Georg-August University; Alemania - Materia
-
EPISTASIS MODEL
GENOMIC PREDICTION
INTERACTION - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/59317
Ver los metadatos del registro completo
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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)Martini, Johannes W. R.Gao, NingCardoso, Diercles F.Wimmer, ValentinErbe, MalenaCantet, Rodolfo Juan CarlosSimianer, HennerEPISTASIS MODELGENOMIC PREDICTIONINTERACTIONhttps://purl.org/becyt/ford/4.2https://purl.org/becyt/ford/4Background: 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.Fil: Martini, Johannes W. R.. Georg-August University; AlemaniaFil: Gao, Ning. Georg-August University; AlemaniaFil: Cardoso, Diercles F.. Georg-August University; AlemaniaFil: Wimmer, Valentin. KWS SAAT SE; AlemaniaFil: Erbe, Malena. Georg-August University; AlemaniaFil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; ArgentinaFil: Simianer, Henner. Georg-August University; AlemaniaBioMed Central2017-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/59317Martini, Johannes W. R.; Gao, Ning; Cardoso, Diercles F.; Wimmer, Valentin; Erbe, Malena; et al.; Genomic prediction with epistasis models: On the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE); BioMed Central; BMC Bioinformatics; 18; 1; 1-20171471-2105CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-016-1439-1info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1439-1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:35:47Zoai:ri.conicet.gov.ar:11336/59317instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:35:48.06CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
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. EPISTASIS MODEL GENOMIC PREDICTION 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) |
dc.creator.none.fl_str_mv |
Martini, Johannes W. R. Gao, Ning Cardoso, Diercles F. Wimmer, Valentin Erbe, Malena Cantet, Rodolfo Juan Carlos Simianer, Henner |
author |
Martini, Johannes W. R. |
author_facet |
Martini, Johannes W. R. Gao, Ning Cardoso, Diercles F. Wimmer, Valentin Erbe, Malena Cantet, Rodolfo Juan Carlos Simianer, Henner |
author_role |
author |
author2 |
Gao, Ning Cardoso, Diercles F. Wimmer, Valentin Erbe, Malena Cantet, Rodolfo Juan Carlos Simianer, Henner |
author2_role |
author author author author author author |
dc.subject.none.fl_str_mv |
EPISTASIS MODEL GENOMIC PREDICTION INTERACTION |
topic |
EPISTASIS MODEL GENOMIC PREDICTION INTERACTION |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/4.2 https://purl.org/becyt/ford/4 |
dc.description.none.fl_txt_mv |
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. Fil: Martini, Johannes W. R.. Georg-August University; Alemania Fil: Gao, Ning. Georg-August University; Alemania Fil: Cardoso, Diercles F.. Georg-August University; Alemania Fil: Wimmer, Valentin. KWS SAAT SE; Alemania Fil: Erbe, Malena. Georg-August University; Alemania Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina Fil: Simianer, Henner. Georg-August University; Alemania |
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 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/59317 Martini, Johannes W. R.; Gao, Ning; Cardoso, Diercles F.; Wimmer, Valentin; Erbe, Malena; et al.; Genomic prediction with epistasis models: On the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE); BioMed Central; BMC Bioinformatics; 18; 1; 1-2017 1471-2105 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/59317 |
identifier_str_mv |
Martini, Johannes W. R.; Gao, Ning; Cardoso, Diercles F.; Wimmer, Valentin; Erbe, Malena; et al.; Genomic prediction with epistasis models: On the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE); BioMed Central; BMC Bioinformatics; 18; 1; 1-2017 1471-2105 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-016-1439-1 info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1439-1 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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score |
13.070432 |