Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.

LOURENCO, D.A.L. - FRAGOMENI, B.O. - TSURUTA, S. - AGUILAR, I. - ZUMBACH, B. - HAWKEN, R.J. - LEGARRA, A. - MISZTAL, I.

Resumen:

ABSTRACT.Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy,whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous thanin dairy cattle.Methods: We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) wereused to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.Results: Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.Conclusions: Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.© 2015 Lourenco et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.


Detalles Bibliográficos
2015
POLLO DE ENGORDE
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53861&biblioteca=vazio&busca=53861&qFacets=53861
Acceso abierto
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author LOURENCO, D.A.L.
author2 FRAGOMENI, B.O.
TSURUTA, S.
AGUILAR, I.
ZUMBACH, B.
HAWKEN, R.J.
LEGARRA, A.
MISZTAL, I.
author2_role author
author
author
author
author
author
author
author_facet LOURENCO, D.A.L.
FRAGOMENI, B.O.
TSURUTA, S.
AGUILAR, I.
ZUMBACH, B.
HAWKEN, R.J.
LEGARRA, A.
MISZTAL, I.
author_role author
bitstream.checksum.fl_str_mv 09d5e5cf4582674abe35c19e1fe9c7e3
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2456/1/sword-2022-12-16T17%3a41%3a42.original.xml
collection AINFO
dc.creator.none.fl_str_mv LOURENCO, D.A.L.
FRAGOMENI, B.O.
TSURUTA, S.
AGUILAR, I.
ZUMBACH, B.
HAWKEN, R.J.
LEGARRA, A.
MISZTAL, I.
dc.date.accessioned.none.fl_str_mv 2022-12-16T20:41:42Z
dc.date.available.none.fl_str_mv 2022-12-16T20:41:42Z
dc.date.issued.none.fl_str_mv 2015
dc.date.updated.none.fl_str_mv 2022-12-16T20:41:42Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy,whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous thanin dairy cattle.Methods: We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) wereused to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.Results: Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.Conclusions: Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.© 2015 Lourenco et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53861&biblioteca=vazio&busca=53861&qFacets=53861
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 POLLO DE ENGORDE
dc.title.none.fl_str_mv Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
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.Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy,whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous thanin dairy cattle.Methods: We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) wereused to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.Results: Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.Conclusions: Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.© 2015 Lourenco et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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repository.name.fl_str_mv AINFO - Instituto Nacional de Investigación Agropecuaria
repository_id_str
rights_invalid_str_mv Acceso abierto
spelling 2022-12-16T20:41:42Z2022-12-16T20:41:42Z20152022-12-16T20:41:42Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=53861&biblioteca=vazio&busca=53861&qFacets=53861ABSTRACT.Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy,whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous thanin dairy cattle.Methods: We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) wereused to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.Results: Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.Conclusions: Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.© 2015 Lourenco et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.https://hdl.handle.net/20.500.12381/2456enenginfo:eu-repo/semantics/openAccessAcceso abiertoPOLLO DE ENGORDEAccuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaLOURENCO, D.A.L.FRAGOMENI, B.O.TSURUTA, S.AGUILAR, I.ZUMBACH, B.HAWKEN, R.J.LEGARRA, A.MISZTAL, I.SWORDsword-2022-12-16T17:41:42.original.xmlOriginal SWORD entry documentapplication/octet-stream3545https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2456/1/sword-2022-12-16T17%3a41%3a42.original.xml09d5e5cf4582674abe35c19e1fe9c7e3MD5120.500.12381/24562022-12-16 17:41:43.348oai:redi.anii.org.uy:20.500.12381/2456Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-12-16T20:41:43AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
LOURENCO, D.A.L.
POLLO DE ENGORDE
status_str publishedVersion
title Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
title_full Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
title_fullStr Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
title_full_unstemmed Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
title_short Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
title_sort Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken.
topic POLLO DE ENGORDE
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=53861&biblioteca=vazio&busca=53861&qFacets=53861