The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure

Autores
Martini, Johannes W. R.; Schrauf, Matías Florián; García Baccino, Carolina Andrea; Pimentel, Eduardo C. G.; Munilla Leguizamon, Sebastian; Rogberg Muñoz, Andres; Cantet, Rodolfo Juan Carlos; Reimer, Christian; Gao, Ning; Wimmer, Valentin; Simianer, Henner
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: The single-step covariance matrix H combines the pedigree-based relationship matrix A with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix G. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights ℑ and ω have been introduced in the definition of H-1, which blend the inverse of a part of A with the inverse of G . Since the definition of this blending is based on the equation describing H-1, its impact on the structure of H is not obvious. In a joint discussion, we considered the question of the shape of H for non-trivial ℑ and ω. Results: Here, we present the general matrix H as a function of these parameters and discuss its structure and properties. Moreover, we screen for optimal values of ℑ and ω with respect to predictive ability, inflation and iterations up to convergence on a well investigated, publicly available wheat data set. Conclusion: Our results may help the reader to develop a better understanding for the effects of changes of ℑ and ω on the covariance model. In particular, we give theoretical arguments that as a general tendency, inflation will be reduced by increasing ℑ or by decreasing ω.
Fil: Martini, Johannes W. R.. KWS SAAT SE; Alemania
Fil: Schrauf, Matías Florián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pimentel, Eduardo C. G.. Bavarian State Research Center for Agriculture; Alemania
Fil: Munilla Leguizamon, Sebastian. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Rogberg Muñoz, Andres. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. 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: Reimer, Christian. University of Goettingen; Alemania
Fil: Gao, Ning. University of Goettingen; Alemania. South China Agricultural University; China
Fil: Wimmer, Valentin. KWS SAAT SE; Alemania
Fil: Simianer, Henner. University of Goettingen; Alemania
Materia
SINGLE STEP
TUNING PARAMETERS
GENOMIC SELECTION
MATRIX INVERSE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/91410
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/91410
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedureMartini, Johannes W. R.Schrauf, Matías FloriánGarcía Baccino, Carolina AndreaPimentel, Eduardo C. G.Munilla Leguizamon, SebastianRogberg Muñoz, AndresCantet, Rodolfo Juan CarlosReimer, ChristianGao, NingWimmer, ValentinSimianer, HennerSINGLE STEPTUNING PARAMETERSGENOMIC SELECTIONMATRIX INVERSEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4https://purl.org/becyt/ford/1.1https://purl.org/becyt/ford/1Background: The single-step covariance matrix H combines the pedigree-based relationship matrix A with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix G. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights ℑ and ω have been introduced in the definition of H-1, which blend the inverse of a part of A with the inverse of G . Since the definition of this blending is based on the equation describing H-1, its impact on the structure of H is not obvious. In a joint discussion, we considered the question of the shape of H for non-trivial ℑ and ω. Results: Here, we present the general matrix H as a function of these parameters and discuss its structure and properties. Moreover, we screen for optimal values of ℑ and ω with respect to predictive ability, inflation and iterations up to convergence on a well investigated, publicly available wheat data set. Conclusion: Our results may help the reader to develop a better understanding for the effects of changes of ℑ and ω on the covariance model. In particular, we give theoretical arguments that as a general tendency, inflation will be reduced by increasing ℑ or by decreasing ω.Fil: Martini, Johannes W. R.. KWS SAAT SE; AlemaniaFil: Schrauf, Matías Florián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pimentel, Eduardo C. G.. Bavarian State Research Center for Agriculture; AlemaniaFil: Munilla Leguizamon, Sebastian. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rogberg Muñoz, Andres. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. 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: Reimer, Christian. University of Goettingen; AlemaniaFil: Gao, Ning. University of Goettingen; Alemania. South China Agricultural University; ChinaFil: Wimmer, Valentin. KWS SAAT SE; AlemaniaFil: Simianer, Henner. University of Goettingen; AlemaniaBioMed Central2018-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/91410Martini, Johannes W. R.; Schrauf, Matías Florián; García Baccino, Carolina Andrea; Pimentel, Eduardo C. G.; Munilla Leguizamon, Sebastian; et al.; The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure; BioMed Central; Genetics Selection Evolution; 50; 1; 4-2018; 1-91297-9686CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-018-0386-xinfo:eu-repo/semantics/altIdentifier/url/https://gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0386-xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:27:45Zoai:ri.conicet.gov.ar:11336/91410instacron: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 10:27:45.966CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
title The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
spellingShingle The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
Martini, Johannes W. R.
SINGLE STEP
TUNING PARAMETERS
GENOMIC SELECTION
MATRIX INVERSE
title_short The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
title_full The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
title_fullStr The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
title_full_unstemmed The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
title_sort The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure
dc.creator.none.fl_str_mv Martini, Johannes W. R.
Schrauf, Matías Florián
García Baccino, Carolina Andrea
Pimentel, Eduardo C. G.
Munilla Leguizamon, Sebastian
Rogberg Muñoz, Andres
Cantet, Rodolfo Juan Carlos
Reimer, Christian
Gao, Ning
Wimmer, Valentin
Simianer, Henner
author Martini, Johannes W. R.
author_facet Martini, Johannes W. R.
Schrauf, Matías Florián
García Baccino, Carolina Andrea
Pimentel, Eduardo C. G.
Munilla Leguizamon, Sebastian
Rogberg Muñoz, Andres
Cantet, Rodolfo Juan Carlos
Reimer, Christian
Gao, Ning
Wimmer, Valentin
Simianer, Henner
author_role author
author2 Schrauf, Matías Florián
García Baccino, Carolina Andrea
Pimentel, Eduardo C. G.
Munilla Leguizamon, Sebastian
Rogberg Muñoz, Andres
Cantet, Rodolfo Juan Carlos
Reimer, Christian
Gao, Ning
Wimmer, Valentin
Simianer, Henner
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv SINGLE STEP
TUNING PARAMETERS
GENOMIC SELECTION
MATRIX INVERSE
topic SINGLE STEP
TUNING PARAMETERS
GENOMIC SELECTION
MATRIX INVERSE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
https://purl.org/becyt/ford/1.1
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: The single-step covariance matrix H combines the pedigree-based relationship matrix A with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix G. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights ℑ and ω have been introduced in the definition of H-1, which blend the inverse of a part of A with the inverse of G . Since the definition of this blending is based on the equation describing H-1, its impact on the structure of H is not obvious. In a joint discussion, we considered the question of the shape of H for non-trivial ℑ and ω. Results: Here, we present the general matrix H as a function of these parameters and discuss its structure and properties. Moreover, we screen for optimal values of ℑ and ω with respect to predictive ability, inflation and iterations up to convergence on a well investigated, publicly available wheat data set. Conclusion: Our results may help the reader to develop a better understanding for the effects of changes of ℑ and ω on the covariance model. In particular, we give theoretical arguments that as a general tendency, inflation will be reduced by increasing ℑ or by decreasing ω.
Fil: Martini, Johannes W. R.. KWS SAAT SE; Alemania
Fil: Schrauf, Matías Florián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pimentel, Eduardo C. G.. Bavarian State Research Center for Agriculture; Alemania
Fil: Munilla Leguizamon, Sebastian. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Rogberg Muñoz, Andres. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. 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: Reimer, Christian. University of Goettingen; Alemania
Fil: Gao, Ning. University of Goettingen; Alemania. South China Agricultural University; China
Fil: Wimmer, Valentin. KWS SAAT SE; Alemania
Fil: Simianer, Henner. University of Goettingen; Alemania
description Background: The single-step covariance matrix H combines the pedigree-based relationship matrix A with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix G. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights ℑ and ω have been introduced in the definition of H-1, which blend the inverse of a part of A with the inverse of G . Since the definition of this blending is based on the equation describing H-1, its impact on the structure of H is not obvious. In a joint discussion, we considered the question of the shape of H for non-trivial ℑ and ω. Results: Here, we present the general matrix H as a function of these parameters and discuss its structure and properties. Moreover, we screen for optimal values of ℑ and ω with respect to predictive ability, inflation and iterations up to convergence on a well investigated, publicly available wheat data set. Conclusion: Our results may help the reader to develop a better understanding for the effects of changes of ℑ and ω on the covariance model. In particular, we give theoretical arguments that as a general tendency, inflation will be reduced by increasing ℑ or by decreasing ω.
publishDate 2018
dc.date.none.fl_str_mv 2018-04
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/11336/91410
Martini, Johannes W. R.; Schrauf, Matías Florián; García Baccino, Carolina Andrea; Pimentel, Eduardo C. G.; Munilla Leguizamon, Sebastian; et al.; The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure; BioMed Central; Genetics Selection Evolution; 50; 1; 4-2018; 1-9
1297-9686
CONICET Digital
CONICET
url http://hdl.handle.net/11336/91410
identifier_str_mv Martini, Johannes W. R.; Schrauf, Matías Florián; García Baccino, Carolina Andrea; Pimentel, Eduardo C. G.; Munilla Leguizamon, Sebastian; et al.; The effect of the H -1 scaling factors τ and ω on the structure of H in the single-step procedure; BioMed Central; Genetics Selection Evolution; 50; 1; 4-2018; 1-9
1297-9686
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/s12711-018-0386-x
info:eu-repo/semantics/altIdentifier/url/https://gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0386-x
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
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)
collection CONICET Digital (CONICET)
instname_str 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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