Training population optimization for genomic selection.
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).
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 |
_version_ | 1805580523342397440 |
---|---|
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 |
bitstream.checksum.fl_str_mv | be5beb0deac379c2363c13f78c651127 |
bitstream.checksumAlgorithm.fl_str_mv | MD5 |
bitstream.url.fl_str_mv | https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1144/1/sword-2022-10-20T22%3a28%3a44.original.xml |
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). |
eu_rights_str_mv | openAccess |
format | article |
id | INIAOAI_d7b9c650e04f4d90587609ed6c98914b |
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 |
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oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/1144 |
publishDate | 2019 |
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 | 2022-10-21T01:28:44Z2022-10-21T01:28:44Z20192022-10-21T01:28:44Zhttp://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 |