Training population optimization for genomic selection.

BERRO, I. - LADO, B. - NALIN, R.S. - QUINCKE, M. - GUTIÉRREZ, L.

Resumen:

ABSTRACT :The effectiveness of genomic selection in breeding programs depends on the phenotypic quality and depth, the prediction model, the number and type of molecular markers, and the size and composition of the training population (TR). Furthermore, population structure and diversity have a key role in the composition of the optimal training sets. Our goal was to compare strategies for optimizing the TR for specific testing populations (TE). A total of 1353 wheat (Triticum aestivum L.) and 644 rice (Oryza sativa L.) advanced lines were evaluated for grain yield in multiple environments. Several within-TR optimization strategies were compared to identify groups of individuals with increased predictive ability. Additionally, optimization strategies to choose individuals from the TR with higher predictive ability for a specific TE were compared. There is a benefit in considering both the population structure and the relationship between the TR and the TE when designing an optimal TR for genomic selection. A weighted relationship matrix with stratified sampling is the best strategy for forward predictions of quantitative traits in populations several generations apart. Genomic selection (GS) consists of selecting individuals from a TE on the basis of genotypic values predicted from their genome-wide molecular marker scores and a statistical model adjusted with individuals that have phenotypic and genotypic information (Meuwissen et al., 2001). The group of individuals that were phenotyped and genotyped is called the TR (Heffner et al. 2009).


Detalles Bibliográficos
2019
SELECCIÓN GENÓMICA
GENOMIC SELECTION
TRIGO
TRITICUM AESTIVUM
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=60511&biblioteca=vazio&busca=60511&qFacets=60511
Acceso abierto
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author BERRO, I.
author2 LADO, B.
NALIN, R.S.
QUINCKE, M.
GUTIÉRREZ, L.
author2_role author
author
author
author
author_facet BERRO, I.
LADO, B.
NALIN, R.S.
QUINCKE, M.
GUTIÉRREZ, L.
author_role author
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bitstream.checksumAlgorithm.fl_str_mv MD5
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collection AINFO
dc.creator.none.fl_str_mv BERRO, I.
LADO, B.
NALIN, R.S.
QUINCKE, M.
GUTIÉRREZ, L.
dc.date.accessioned.none.fl_str_mv 2022-10-21T01:28:44Z
dc.date.available.none.fl_str_mv 2022-10-21T01:28:44Z
dc.date.issued.none.fl_str_mv 2019
dc.date.updated.none.fl_str_mv 2022-10-21T01:28:44Z
dc.description.abstract.none.fl_txt_mv ABSTRACT :The effectiveness of genomic selection in breeding programs depends on the phenotypic quality and depth, the prediction model, the number and type of molecular markers, and the size and composition of the training population (TR). Furthermore, population structure and diversity have a key role in the composition of the optimal training sets. Our goal was to compare strategies for optimizing the TR for specific testing populations (TE). A total of 1353 wheat (Triticum aestivum L.) and 644 rice (Oryza sativa L.) advanced lines were evaluated for grain yield in multiple environments. Several within-TR optimization strategies were compared to identify groups of individuals with increased predictive ability. Additionally, optimization strategies to choose individuals from the TR with higher predictive ability for a specific TE were compared. There is a benefit in considering both the population structure and the relationship between the TR and the TE when designing an optimal TR for genomic selection. A weighted relationship matrix with stratified sampling is the best strategy for forward predictions of quantitative traits in populations several generations apart. Genomic selection (GS) consists of selecting individuals from a TE on the basis of genotypic values predicted from their genome-wide molecular marker scores and a statistical model adjusted with individuals that have phenotypic and genotypic information (Meuwissen et al., 2001). The group of individuals that were phenotyped and genotyped is called the TR (Heffner et al. 2009).
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=60511&biblioteca=vazio&busca=60511&qFacets=60511
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 SELECCIÓN GENÓMICA
GENOMIC SELECTION
TRIGO
TRITICUM AESTIVUM
dc.title.none.fl_str_mv Training population optimization for genomic selection.
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 :The effectiveness of genomic selection in breeding programs depends on the phenotypic quality and depth, the prediction model, the number and type of molecular markers, and the size and composition of the training population (TR). Furthermore, population structure and diversity have a key role in the composition of the optimal training sets. Our goal was to compare strategies for optimizing the TR for specific testing populations (TE). A total of 1353 wheat (Triticum aestivum L.) and 644 rice (Oryza sativa L.) advanced lines were evaluated for grain yield in multiple environments. Several within-TR optimization strategies were compared to identify groups of individuals with increased predictive ability. Additionally, optimization strategies to choose individuals from the TR with higher predictive ability for a specific TE were compared. There is a benefit in considering both the population structure and the relationship between the TR and the TE when designing an optimal TR for genomic selection. A weighted relationship matrix with stratified sampling is the best strategy for forward predictions of quantitative traits in populations several generations apart. Genomic selection (GS) consists of selecting individuals from a TE on the basis of genotypic values predicted from their genome-wide molecular marker scores and a statistical model adjusted with individuals that have phenotypic and genotypic information (Meuwissen et al., 2001). The group of individuals that were phenotyped and genotyped is called the TR (Heffner et al. 2009).
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spelling 2022-10-21T01:28:44Z2022-10-21T01:28:44Z20192022-10-21T01:28:44Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=60511&biblioteca=vazio&busca=60511&qFacets=60511ABSTRACT :The effectiveness of genomic selection in breeding programs depends on the phenotypic quality and depth, the prediction model, the number and type of molecular markers, and the size and composition of the training population (TR). Furthermore, population structure and diversity have a key role in the composition of the optimal training sets. Our goal was to compare strategies for optimizing the TR for specific testing populations (TE). A total of 1353 wheat (Triticum aestivum L.) and 644 rice (Oryza sativa L.) advanced lines were evaluated for grain yield in multiple environments. Several within-TR optimization strategies were compared to identify groups of individuals with increased predictive ability. Additionally, optimization strategies to choose individuals from the TR with higher predictive ability for a specific TE were compared. There is a benefit in considering both the population structure and the relationship between the TR and the TE when designing an optimal TR for genomic selection. A weighted relationship matrix with stratified sampling is the best strategy for forward predictions of quantitative traits in populations several generations apart. Genomic selection (GS) consists of selecting individuals from a TE on the basis of genotypic values predicted from their genome-wide molecular marker scores and a statistical model adjusted with individuals that have phenotypic and genotypic information (Meuwissen et al., 2001). The group of individuals that were phenotyped and genotyped is called the TR (Heffner et al. 2009).https://hdl.handle.net/20.500.12381/1144enenginfo:eu-repo/semantics/openAccessAcceso abiertoSELECCIÓN GENÓMICAGENOMIC SELECTIONTRIGOTRITICUM AESTIVUMTraining population optimization for genomic selection.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaBERRO, I.LADO, B.NALIN, R.S.QUINCKE, M.GUTIÉRREZ, L.SWORDsword-2022-10-20T22:28:44.original.xmlOriginal SWORD entry documentapplication/octet-stream2639https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1144/1/sword-2022-10-20T22%3a28%3a44.original.xmlbe5beb0deac379c2363c13f78c651127MD5120.500.12381/11442022-10-20 22:28:45.367oai:redi.anii.org.uy:20.500.12381/1144Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:28:45AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Training population optimization for genomic selection.
BERRO, I.
SELECCIÓN GENÓMICA
GENOMIC SELECTION
TRIGO
TRITICUM AESTIVUM
status_str publishedVersion
title Training population optimization for genomic selection.
title_full Training population optimization for genomic selection.
title_fullStr Training population optimization for genomic selection.
title_full_unstemmed Training population optimization for genomic selection.
title_short Training population optimization for genomic selection.
title_sort Training population optimization for genomic selection.
topic SELECCIÓN GENÓMICA
GENOMIC SELECTION
TRIGO
TRITICUM AESTIVUM
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=60511&biblioteca=vazio&busca=60511&qFacets=60511