Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS.
Resumen:
ABSTRACT.Three different procedures were implemented to calculate weights for a genomic relationship matrix to restrict the shrinkage along iterations of weighted single-step genomic BLUP (WssGBLUP). The procedures as well as BayesC were tested with 3 simulated data sets. Prediction accuracy for WssGBLUP improved at 2nd or 3rd iteration by updating only the top number of SNP equal to 1 × or 3 × the number of QTL; accuracy increased after 3rd iteration and remained stable by using weights proportional to 2pi(1- pi)ui2+ constant. Except in the 5 QTL scenario, accuracies with all WssGBLUP procedures were higher than with BayesC. Noise in Manhattan plots was small with 5 and 100 QTL but large with 500 QTL.
| 2014 | |
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GWAS WssGBLUP |
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| Inglés | |
| Instituto Nacional de Investigación Agropecuaria | |
| AINFO | |
| http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61922&biblioteca=vazio&busca=61922&qFacets=61922 | |
| Acceso abierto |
| _version_ | 1805580533649899520 |
|---|---|
| author | ZHANG, X. |
| author2 | LOURENCO, D. MISZTAL, I. AGUILAR, I. LEGARRA, A. |
| author2_role | author author author author |
| author_facet | ZHANG, X. LOURENCO, D. MISZTAL, I. AGUILAR, I. LEGARRA, A. |
| author_role | author |
| bitstream.checksum.fl_str_mv | bae1207afdf97504c6ed84f4f53ee37e |
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| bitstream.url.fl_str_mv | https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1731/1/sword-2022-10-20T22%3a48%3a59.original.xml |
| collection | AINFO |
| dc.creator.none.fl_str_mv | ZHANG, X. LOURENCO, D. MISZTAL, I. AGUILAR, I. LEGARRA, A. |
| dc.date.accessioned.none.fl_str_mv | 2022-10-21T01:48:59Z |
| dc.date.available.none.fl_str_mv | 2022-10-21T01:48:59Z |
| dc.date.issued.none.fl_str_mv | 2014 |
| dc.date.updated.none.fl_str_mv | 2022-10-21T01:48:59Z |
| dc.description.abstract.none.fl_txt_mv | ABSTRACT.Three different procedures were implemented to calculate weights for a genomic relationship matrix to restrict the shrinkage along iterations of weighted single-step genomic BLUP (WssGBLUP). The procedures as well as BayesC were tested with 3 simulated data sets. Prediction accuracy for WssGBLUP improved at 2nd or 3rd iteration by updating only the top number of SNP equal to 1 × or 3 × the number of QTL; accuracy increased after 3rd iteration and remained stable by using weights proportional to 2pi(1- pi)ui2+ constant. Except in the 5 QTL scenario, accuracies with all WssGBLUP procedures were higher than with BayesC. Noise in Manhattan plots was small with 5 and 100 QTL but large with 500 QTL. |
| dc.identifier.none.fl_str_mv | http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61922&biblioteca=vazio&busca=61922&qFacets=61922 |
| 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 | GWAS WssGBLUP |
| dc.title.none.fl_str_mv | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| dc.type.none.fl_str_mv | ConferenceObject PublishedVersion info:eu-repo/semantics/conferenceObject |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | ABSTRACT.Three different procedures were implemented to calculate weights for a genomic relationship matrix to restrict the shrinkage along iterations of weighted single-step genomic BLUP (WssGBLUP). The procedures as well as BayesC were tested with 3 simulated data sets. Prediction accuracy for WssGBLUP improved at 2nd or 3rd iteration by updating only the top number of SNP equal to 1 × or 3 × the number of QTL; accuracy increased after 3rd iteration and remained stable by using weights proportional to 2pi(1- pi)ui2+ constant. Except in the 5 QTL scenario, accuracies with all WssGBLUP procedures were higher than with BayesC. Noise in Manhattan plots was small with 5 and 100 QTL but large with 500 QTL. |
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| 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:20.500.12381/1731 |
| publishDate | 2014 |
| 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 | 2022-10-21T01:48:59Z2022-10-21T01:48:59Z20142022-10-21T01:48:59Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=61922&biblioteca=vazio&busca=61922&qFacets=61922ABSTRACT.Three different procedures were implemented to calculate weights for a genomic relationship matrix to restrict the shrinkage along iterations of weighted single-step genomic BLUP (WssGBLUP). The procedures as well as BayesC were tested with 3 simulated data sets. Prediction accuracy for WssGBLUP improved at 2nd or 3rd iteration by updating only the top number of SNP equal to 1 × or 3 × the number of QTL; accuracy increased after 3rd iteration and remained stable by using weights proportional to 2pi(1- pi)ui2+ constant. Except in the 5 QTL scenario, accuracies with all WssGBLUP procedures were higher than with BayesC. Noise in Manhattan plots was small with 5 and 100 QTL but large with 500 QTL.https://hdl.handle.net/20.500.12381/1731enenginfo:eu-repo/semantics/openAccessAcceso abiertoGWASWssGBLUPWeighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS.ConferenceObjectPublishedVersioninfo:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaZHANG, X.LOURENCO, D.MISZTAL, I.AGUILAR, I.LEGARRA, A.SWORDsword-2022-10-20T22:48:59.original.xmlOriginal SWORD entry documentapplication/octet-stream1715https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1731/1/sword-2022-10-20T22%3a48%3a59.original.xmlbae1207afdf97504c6ed84f4f53ee37eMD5120.500.12381/17312022-10-20 22:48:59.975oai:redi.anii.org.uy:20.500.12381/1731Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:48:59AINFO - Instituto Nacional de Investigación Agropecuariafalse |
| spellingShingle | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. ZHANG, X. GWAS WssGBLUP |
| status_str | publishedVersion |
| title | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| title_full | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| title_fullStr | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| title_full_unstemmed | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| title_short | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| title_sort | Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. |
| topic | GWAS WssGBLUP |
| url | http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61922&biblioteca=vazio&busca=61922&qFacets=61922 |
