Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.

FRAGOMENI, B.O. - LOURENCO, D.A.L. - TSURUTA, S. - MASUDA, Y. - AGUILAR, I. - LEGARRA, A. - LAWLOR, T.J. - MIZTAL, I.

Resumen:

ABSTRACT.The purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with >5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires + cows (50,000), only cows (27,000), or sires with >5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy. © 2015 American Dairy Science Association.


Detalles Bibliográficos
2015
ANIMALIA
SINGLE-STEP GENOMIC BLUP
GENOMIC RECURSION
GENOMIC SELECTION
MEJORAMIENTO GENETICO ANIMAL
BLUP
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53873&biblioteca=vazio&busca=53873&qFacets=53873
Acceso abierto
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author FRAGOMENI, B.O.
author2 LOURENCO, D.A.L.
TSURUTA, S.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
LAWLOR, T.J.
MIZTAL, I.
author2_role author
author
author
author
author
author
author
author_facet FRAGOMENI, B.O.
LOURENCO, D.A.L.
TSURUTA, S.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
LAWLOR, T.J.
MIZTAL, I.
author_role author
bitstream.checksum.fl_str_mv f1a2c73e556e4f6b1b26d7d191b99a1f
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2458/1/sword-2022-12-16T17%3a41%3a47.original.xml
collection AINFO
dc.creator.none.fl_str_mv FRAGOMENI, B.O.
LOURENCO, D.A.L.
TSURUTA, S.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
LAWLOR, T.J.
MIZTAL, I.
dc.date.accessioned.none.fl_str_mv 2022-12-16T20:41:47Z
dc.date.available.none.fl_str_mv 2022-12-16T20:41:47Z
dc.date.issued.none.fl_str_mv 2015
dc.date.updated.none.fl_str_mv 2022-12-16T20:41:47Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.The purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with >5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires + cows (50,000), only cows (27,000), or sires with >5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy. © 2015 American Dairy Science Association.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53873&biblioteca=vazio&busca=53873&qFacets=53873
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 ANIMALIA
SINGLE-STEP GENOMIC BLUP
GENOMIC RECURSION
GENOMIC SELECTION
MEJORAMIENTO GENETICO ANIMAL
BLUP
dc.title.none.fl_str_mv Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
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 purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with >5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires + cows (50,000), only cows (27,000), or sires with >5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy. © 2015 American Dairy Science Association.
eu_rights_str_mv openAccess
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spelling 2022-12-16T20:41:47Z2022-12-16T20:41:47Z20152022-12-16T20:41:47Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=53873&biblioteca=vazio&busca=53873&qFacets=53873ABSTRACT.The purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with >5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires + cows (50,000), only cows (27,000), or sires with >5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy. © 2015 American Dairy Science Association.https://hdl.handle.net/20.500.12381/2458enenginfo:eu-repo/semantics/openAccessAcceso abiertoANIMALIASINGLE-STEP GENOMIC BLUPGENOMIC RECURSIONGENOMIC SELECTIONMEJORAMIENTO GENETICO ANIMALBLUPHot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaFRAGOMENI, B.O.LOURENCO, D.A.L.TSURUTA, S.MASUDA, Y.AGUILAR, I.LEGARRA, A.LAWLOR, T.J.MIZTAL, I.SWORDsword-2022-12-16T17:41:47.original.xmlOriginal SWORD entry documentapplication/octet-stream3307https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2458/1/sword-2022-12-16T17%3a41%3a47.original.xmlf1a2c73e556e4f6b1b26d7d191b99a1fMD5120.500.12381/24582022-12-16 17:41:48.11oai:redi.anii.org.uy:20.500.12381/2458Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-12-16T20:41:48AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
FRAGOMENI, B.O.
ANIMALIA
SINGLE-STEP GENOMIC BLUP
GENOMIC RECURSION
GENOMIC SELECTION
MEJORAMIENTO GENETICO ANIMAL
BLUP
status_str publishedVersion
title Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
title_full Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
title_fullStr Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
title_full_unstemmed Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
title_short Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
title_sort Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes.
topic ANIMALIA
SINGLE-STEP GENOMIC BLUP
GENOMIC RECURSION
GENOMIC SELECTION
MEJORAMIENTO GENETICO ANIMAL
BLUP
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53873&biblioteca=vazio&busca=53873&qFacets=53873