Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.

LOURENCO, D. - TSURUTA, S. - FRAGOMENI, B. - MASUDA, Y. - AGUILAR, I. - LEGARRA, A. - MILLER, S. - MOSER, D. - MISZTAL, I.

Resumen:

ABSTRACT.The objective of this study was to implement single-step genomic BLUP (ssGBLUP) for national Angus cattle evaluation in the US. National evaluations include a variety of models with several linear and categorical traits, maternal effects, multibreed data, and a large number of genotyped animals. For the initial investigation, we used a dataset from 2014 that comprised over 8 million animals, 6 million birth weight (BW) and weaning weight (WW) records, 3.4 million post-weaning gain (PWG) records, and genotypes for 52k animals. A dataset from 2017 was later used that included 335k genotyped animals. The ability to predict future performance of young animals was investigated when using regular BLUP and ssGBLUP. Because of the increasing number of genotyped animals and the high computing cost to invert the genomic relationship matrix (G), the algorithm for proven and young (APY) was used to approximate the inverse of G. The APY uses recursions on a small subset of genotyped animals, called core. We further tested the feasibility of having daily interim genomic predictions for newly-genotyped animals based on SNP effects derived from the previous official ssGBLUP evaluation. In addition, we extended all models used in traditional evaluations to ssGBLUP, and compared genetic trends from traditional BLUP, ssGBLUP, and a multistep method that was implemented for the American Angus genomic evaluation in 2009. A new algorithm to approximate accuracy of GEBV for large genomic data was also developed. On average, the increase in ability to predict future performance, for BW, WW, and PWG, with ssGBLUP was 25% in the 2014 data and 36% in the 2017 data, compared to the traditional BLUP. The ssGBLUP with APY was as accurate as the regular ssGBLUP when the number of core animals was at least 10,000, independently of which animals were in the core group. Interim predictions derived from ssGBLUP provided accurate genomic values for newly-genotyped animals. Genetic trends for ssGBLUP and BLUP were similar, revealing overestimation in multistep evaluations, especially for traits with less phenotypes. Single-step GBLUP became a reality for American Angus evaluation and its implementation process resulted in successful updates in methodology, making this approach mature for national beef cattle evaluation. Keywords: algorithm for proven and young, Angus, genomic selection, indirect prediction.


Detalles Bibliográficos
2018
Algorithm for proven and young
Angus
Genomic selection
Indirect prediction
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61912&biblioteca=vazio&busca=61912&qFacets=61912
Acceso abierto
_version_ 1805580524830326784
author LOURENCO, D.
author2 TSURUTA, S.
FRAGOMENI, B.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
MILLER, S.
MOSER, D.
MISZTAL, I.
author2_role author
author
author
author
author
author
author
author
author_facet LOURENCO, D.
TSURUTA, S.
FRAGOMENI, B.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
MILLER, S.
MOSER, D.
MISZTAL, I.
author_role author
bitstream.checksum.fl_str_mv f0b5b8eb195dec0b51c132594c704e92
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collection AINFO
dc.creator.none.fl_str_mv LOURENCO, D.
TSURUTA, S.
FRAGOMENI, B.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
MILLER, S.
MOSER, D.
MISZTAL, I.
dc.date.accessioned.none.fl_str_mv 2022-10-21T01:48:45Z
dc.date.available.none.fl_str_mv 2022-10-21T01:48:45Z
dc.date.issued.none.fl_str_mv 2018
dc.date.updated.none.fl_str_mv 2022-10-21T01:48:45Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.The objective of this study was to implement single-step genomic BLUP (ssGBLUP) for national Angus cattle evaluation in the US. National evaluations include a variety of models with several linear and categorical traits, maternal effects, multibreed data, and a large number of genotyped animals. For the initial investigation, we used a dataset from 2014 that comprised over 8 million animals, 6 million birth weight (BW) and weaning weight (WW) records, 3.4 million post-weaning gain (PWG) records, and genotypes for 52k animals. A dataset from 2017 was later used that included 335k genotyped animals. The ability to predict future performance of young animals was investigated when using regular BLUP and ssGBLUP. Because of the increasing number of genotyped animals and the high computing cost to invert the genomic relationship matrix (G), the algorithm for proven and young (APY) was used to approximate the inverse of G. The APY uses recursions on a small subset of genotyped animals, called core. We further tested the feasibility of having daily interim genomic predictions for newly-genotyped animals based on SNP effects derived from the previous official ssGBLUP evaluation. In addition, we extended all models used in traditional evaluations to ssGBLUP, and compared genetic trends from traditional BLUP, ssGBLUP, and a multistep method that was implemented for the American Angus genomic evaluation in 2009. A new algorithm to approximate accuracy of GEBV for large genomic data was also developed. On average, the increase in ability to predict future performance, for BW, WW, and PWG, with ssGBLUP was 25% in the 2014 data and 36% in the 2017 data, compared to the traditional BLUP. The ssGBLUP with APY was as accurate as the regular ssGBLUP when the number of core animals was at least 10,000, independently of which animals were in the core group. Interim predictions derived from ssGBLUP provided accurate genomic values for newly-genotyped animals. Genetic trends for ssGBLUP and BLUP were similar, revealing overestimation in multistep evaluations, especially for traits with less phenotypes. Single-step GBLUP became a reality for American Angus evaluation and its implementation process resulted in successful updates in methodology, making this approach mature for national beef cattle evaluation. Keywords: algorithm for proven and young, Angus, genomic selection, indirect prediction.
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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
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instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv Algorithm for proven and young
Angus
Genomic selection
Indirect prediction
dc.title.none.fl_str_mv Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
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.The objective of this study was to implement single-step genomic BLUP (ssGBLUP) for national Angus cattle evaluation in the US. National evaluations include a variety of models with several linear and categorical traits, maternal effects, multibreed data, and a large number of genotyped animals. For the initial investigation, we used a dataset from 2014 that comprised over 8 million animals, 6 million birth weight (BW) and weaning weight (WW) records, 3.4 million post-weaning gain (PWG) records, and genotypes for 52k animals. A dataset from 2017 was later used that included 335k genotyped animals. The ability to predict future performance of young animals was investigated when using regular BLUP and ssGBLUP. Because of the increasing number of genotyped animals and the high computing cost to invert the genomic relationship matrix (G), the algorithm for proven and young (APY) was used to approximate the inverse of G. The APY uses recursions on a small subset of genotyped animals, called core. We further tested the feasibility of having daily interim genomic predictions for newly-genotyped animals based on SNP effects derived from the previous official ssGBLUP evaluation. In addition, we extended all models used in traditional evaluations to ssGBLUP, and compared genetic trends from traditional BLUP, ssGBLUP, and a multistep method that was implemented for the American Angus genomic evaluation in 2009. A new algorithm to approximate accuracy of GEBV for large genomic data was also developed. On average, the increase in ability to predict future performance, for BW, WW, and PWG, with ssGBLUP was 25% in the 2014 data and 36% in the 2017 data, compared to the traditional BLUP. The ssGBLUP with APY was as accurate as the regular ssGBLUP when the number of core animals was at least 10,000, independently of which animals were in the core group. Interim predictions derived from ssGBLUP provided accurate genomic values for newly-genotyped animals. Genetic trends for ssGBLUP and BLUP were similar, revealing overestimation in multistep evaluations, especially for traits with less phenotypes. Single-step GBLUP became a reality for American Angus evaluation and its implementation process resulted in successful updates in methodology, making this approach mature for national beef cattle evaluation. Keywords: algorithm for proven and young, Angus, genomic selection, indirect prediction.
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spelling 2022-10-21T01:48:45Z2022-10-21T01:48:45Z20182022-10-21T01:48:45Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=61912&biblioteca=vazio&busca=61912&qFacets=61912ABSTRACT.The objective of this study was to implement single-step genomic BLUP (ssGBLUP) for national Angus cattle evaluation in the US. National evaluations include a variety of models with several linear and categorical traits, maternal effects, multibreed data, and a large number of genotyped animals. For the initial investigation, we used a dataset from 2014 that comprised over 8 million animals, 6 million birth weight (BW) and weaning weight (WW) records, 3.4 million post-weaning gain (PWG) records, and genotypes for 52k animals. A dataset from 2017 was later used that included 335k genotyped animals. The ability to predict future performance of young animals was investigated when using regular BLUP and ssGBLUP. Because of the increasing number of genotyped animals and the high computing cost to invert the genomic relationship matrix (G), the algorithm for proven and young (APY) was used to approximate the inverse of G. The APY uses recursions on a small subset of genotyped animals, called core. We further tested the feasibility of having daily interim genomic predictions for newly-genotyped animals based on SNP effects derived from the previous official ssGBLUP evaluation. In addition, we extended all models used in traditional evaluations to ssGBLUP, and compared genetic trends from traditional BLUP, ssGBLUP, and a multistep method that was implemented for the American Angus genomic evaluation in 2009. A new algorithm to approximate accuracy of GEBV for large genomic data was also developed. On average, the increase in ability to predict future performance, for BW, WW, and PWG, with ssGBLUP was 25% in the 2014 data and 36% in the 2017 data, compared to the traditional BLUP. The ssGBLUP with APY was as accurate as the regular ssGBLUP when the number of core animals was at least 10,000, independently of which animals were in the core group. Interim predictions derived from ssGBLUP provided accurate genomic values for newly-genotyped animals. Genetic trends for ssGBLUP and BLUP were similar, revealing overestimation in multistep evaluations, especially for traits with less phenotypes. Single-step GBLUP became a reality for American Angus evaluation and its implementation process resulted in successful updates in methodology, making this approach mature for national beef cattle evaluation. Keywords: algorithm for proven and young, Angus, genomic selection, indirect prediction.https://hdl.handle.net/20.500.12381/1722enenginfo:eu-repo/semantics/openAccessAcceso abiertoAlgorithm for proven and youngAngusGenomic selectionIndirect predictionSingle-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.ConferenceObjectPublishedVersioninfo:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaLOURENCO, D.TSURUTA, S.FRAGOMENI, B.MASUDA, Y.AGUILAR, I.LEGARRA, A.MILLER, S.MOSER, D.MISZTAL, I.SWORDsword-2022-10-20T22:48:45.original.xmlOriginal SWORD entry documentapplication/octet-stream3773https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1722/1/sword-2022-10-20T22%3a48%3a45.original.xmlf0b5b8eb195dec0b51c132594c704e92MD5120.500.12381/17222022-10-20 22:48:45.46oai:redi.anii.org.uy:20.500.12381/1722Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:48:45AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
LOURENCO, D.
Algorithm for proven and young
Angus
Genomic selection
Indirect prediction
status_str publishedVersion
title Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
title_full Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
title_fullStr Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
title_full_unstemmed Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
title_short Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
title_sort Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation.
topic Algorithm for proven and young
Angus
Genomic selection
Indirect prediction
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61912&biblioteca=vazio&busca=61912&qFacets=61912