Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)

LOURENCO, D. A. L. - TSURUTA, S. - FRAGOMENI, B. O. - MASUDA, Y. - AGUILAR, I. - LEGARRA, A. - BERTRAND, J. K. - AMEN, T. S. - WANG. L. - MOSER, D. W. - MISZTAL, I.

Resumen:

ABSTRACT.Predictive ability of genomic EBV when using single-step genomic BLUP (ssGBLUP) in Angus cattle was investigated. Over 6 million records were available on birth weight (BiW) and weaning weight (WW), almost 3.4 million on postweaning gain (PWG), and over 1.3 million on calving ease (CE). Genomic information was available on, at most, 51,883 animals,which included high and low EBV accuracy animals. Traditional EBV was computed by BLUP and genomic EBV by ssGBLUP and indirect prediction based on SNP effects was derived from ssGBLUP; SNP effects were calculated based on the following reference populations: ref_2k (contains top bulls and top cows that had an EBV accuracy for BiW ≥0.85), ref_8k (contains all parents that were genotyped), and ref_33k (contains all genotyped animals born up to 2012). Indirect prediction was obtained as direct genomic value (DGV) or as anindex of DGV and parent average (PA). Additionally, runs with ssGBLUP used the inverse of the genomic relationship matrix calculated by an algorithm for proven and young animals (APY) that uses recursions on a small subset of reference animals. An extra reference subset included 3,872 genotyped parents of genotyped animals (ref_4k). Cross-validation was used to assess predictive ability on a validation population of 18,721 animals born in 2013. Computations for growth traits used multiple-trait linear model and, for CE, a bivariate CE?BiW threshold-linear model. With BLUP, predictivities were 0.29, 0.34, 0.23, and 0.12 for BiW, WW, PWG, and CE, respectively. With ssGBLUP and ref_2k, predictivities were 0.34, 0.35, 0.27, and 0.13 for BiW, WW, PWG, and CE, respectively, and with ssGBLUP and ref_33k, predictivities were 0.39, 0.38, 0.29, and 0.13 for BiW, WW, PWG, and CE, respectively. Low predictivity for CE was due to low incidence rate of difficult calving. Indirect predictions with ref_33k were as accurate as with full ssGBLUP. Using the APY and recursions on ref_4k gave 88% gains of full ssGBLUP and using the APY and recursions on ref_8k gave 97% gains of full ssGBLUP. Genomic evaluation in beef cattle with ssGBLUP is feasible while keeping the models (maternal, multiple trait, and threshold) already used in regular BLUP. Gains in predictivity are dependent on the composition of the reference population. Indirect predictions via SNP effects derived from ssGBLUP allow for accurate genomic predictions on young animals, with no advantage of including PA inthe index if the reference population is large. With the APY conditioning on about 10,000 reference animals, ssGBLUP is potentially applicable to a large number of genotyped animals without compromising predictive ability. © 2015 American Society of Animal Science. All rights reserved


Detalles Bibliográficos
2015
BEEF CATTLE
GENETIC RESURSION
INDIRECT PREDICTION
GANADO DE CARNE
MEJORAMIENTO GENETICO ANIMAL
GENOMIC SELECTION
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=54005&biblioteca=vazio&busca=54005&qFacets=54005
Acceso abierto
_version_ 1805580522680745984
author LOURENCO, D. A. L.
author2 TSURUTA, S.
FRAGOMENI, B. O.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
BERTRAND, J. K.
AMEN, T. S.
WANG. L.
MOSER, D. W.
MISZTAL, I.
author2_role author
author
author
author
author
author
author
author
author
author
author_facet LOURENCO, D. A. L.
TSURUTA, S.
FRAGOMENI, B. O.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
BERTRAND, J. K.
AMEN, T. S.
WANG. L.
MOSER, D. W.
MISZTAL, I.
author_role author
bitstream.checksum.fl_str_mv d431b16ce6076d75252d724681bdb4e1
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2469/1/sword-2022-12-16T17%3a42%3a17.original.xml
collection AINFO
dc.creator.none.fl_str_mv LOURENCO, D. A. L.
TSURUTA, S.
FRAGOMENI, B. O.
MASUDA, Y.
AGUILAR, I.
LEGARRA, A.
BERTRAND, J. K.
AMEN, T. S.
WANG. L.
MOSER, D. W.
MISZTAL, I.
dc.date.accessioned.none.fl_str_mv 2022-12-16T20:42:17Z
dc.date.available.none.fl_str_mv 2022-12-16T20:42:17Z
dc.date.issued.none.fl_str_mv 2015
dc.date.updated.none.fl_str_mv 2022-12-16T20:42:17Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.Predictive ability of genomic EBV when using single-step genomic BLUP (ssGBLUP) in Angus cattle was investigated. Over 6 million records were available on birth weight (BiW) and weaning weight (WW), almost 3.4 million on postweaning gain (PWG), and over 1.3 million on calving ease (CE). Genomic information was available on, at most, 51,883 animals,which included high and low EBV accuracy animals. Traditional EBV was computed by BLUP and genomic EBV by ssGBLUP and indirect prediction based on SNP effects was derived from ssGBLUP; SNP effects were calculated based on the following reference populations: ref_2k (contains top bulls and top cows that had an EBV accuracy for BiW ≥0.85), ref_8k (contains all parents that were genotyped), and ref_33k (contains all genotyped animals born up to 2012). Indirect prediction was obtained as direct genomic value (DGV) or as anindex of DGV and parent average (PA). Additionally, runs with ssGBLUP used the inverse of the genomic relationship matrix calculated by an algorithm for proven and young animals (APY) that uses recursions on a small subset of reference animals. An extra reference subset included 3,872 genotyped parents of genotyped animals (ref_4k). Cross-validation was used to assess predictive ability on a validation population of 18,721 animals born in 2013. Computations for growth traits used multiple-trait linear model and, for CE, a bivariate CE?BiW threshold-linear model. With BLUP, predictivities were 0.29, 0.34, 0.23, and 0.12 for BiW, WW, PWG, and CE, respectively. With ssGBLUP and ref_2k, predictivities were 0.34, 0.35, 0.27, and 0.13 for BiW, WW, PWG, and CE, respectively, and with ssGBLUP and ref_33k, predictivities were 0.39, 0.38, 0.29, and 0.13 for BiW, WW, PWG, and CE, respectively. Low predictivity for CE was due to low incidence rate of difficult calving. Indirect predictions with ref_33k were as accurate as with full ssGBLUP. Using the APY and recursions on ref_4k gave 88% gains of full ssGBLUP and using the APY and recursions on ref_8k gave 97% gains of full ssGBLUP. Genomic evaluation in beef cattle with ssGBLUP is feasible while keeping the models (maternal, multiple trait, and threshold) already used in regular BLUP. Gains in predictivity are dependent on the composition of the reference population. Indirect predictions via SNP effects derived from ssGBLUP allow for accurate genomic predictions on young animals, with no advantage of including PA inthe index if the reference population is large. With the APY conditioning on about 10,000 reference animals, ssGBLUP is potentially applicable to a large number of genotyped animals without compromising predictive ability. © 2015 American Society of Animal Science. All rights reserved
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=54005&biblioteca=vazio&busca=54005&qFacets=54005
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 BEEF CATTLE
GENETIC RESURSION
INDIRECT PREDICTION
GANADO DE CARNE
MEJORAMIENTO GENETICO ANIMAL
GENOMIC SELECTION
dc.title.none.fl_str_mv Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
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.Predictive ability of genomic EBV when using single-step genomic BLUP (ssGBLUP) in Angus cattle was investigated. Over 6 million records were available on birth weight (BiW) and weaning weight (WW), almost 3.4 million on postweaning gain (PWG), and over 1.3 million on calving ease (CE). Genomic information was available on, at most, 51,883 animals,which included high and low EBV accuracy animals. Traditional EBV was computed by BLUP and genomic EBV by ssGBLUP and indirect prediction based on SNP effects was derived from ssGBLUP; SNP effects were calculated based on the following reference populations: ref_2k (contains top bulls and top cows that had an EBV accuracy for BiW ≥0.85), ref_8k (contains all parents that were genotyped), and ref_33k (contains all genotyped animals born up to 2012). Indirect prediction was obtained as direct genomic value (DGV) or as anindex of DGV and parent average (PA). Additionally, runs with ssGBLUP used the inverse of the genomic relationship matrix calculated by an algorithm for proven and young animals (APY) that uses recursions on a small subset of reference animals. An extra reference subset included 3,872 genotyped parents of genotyped animals (ref_4k). Cross-validation was used to assess predictive ability on a validation population of 18,721 animals born in 2013. Computations for growth traits used multiple-trait linear model and, for CE, a bivariate CE?BiW threshold-linear model. With BLUP, predictivities were 0.29, 0.34, 0.23, and 0.12 for BiW, WW, PWG, and CE, respectively. With ssGBLUP and ref_2k, predictivities were 0.34, 0.35, 0.27, and 0.13 for BiW, WW, PWG, and CE, respectively, and with ssGBLUP and ref_33k, predictivities were 0.39, 0.38, 0.29, and 0.13 for BiW, WW, PWG, and CE, respectively. Low predictivity for CE was due to low incidence rate of difficult calving. Indirect predictions with ref_33k were as accurate as with full ssGBLUP. Using the APY and recursions on ref_4k gave 88% gains of full ssGBLUP and using the APY and recursions on ref_8k gave 97% gains of full ssGBLUP. Genomic evaluation in beef cattle with ssGBLUP is feasible while keeping the models (maternal, multiple trait, and threshold) already used in regular BLUP. Gains in predictivity are dependent on the composition of the reference population. Indirect predictions via SNP effects derived from ssGBLUP allow for accurate genomic predictions on young animals, with no advantage of including PA inthe index if the reference population is large. With the APY conditioning on about 10,000 reference animals, ssGBLUP is potentially applicable to a large number of genotyped animals without compromising predictive ability. © 2015 American Society of Animal Science. All rights reserved
eu_rights_str_mv openAccess
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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 2022-12-16T20:42:17Z2022-12-16T20:42:17Z20152022-12-16T20:42:17Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=54005&biblioteca=vazio&busca=54005&qFacets=54005ABSTRACT.Predictive ability of genomic EBV when using single-step genomic BLUP (ssGBLUP) in Angus cattle was investigated. Over 6 million records were available on birth weight (BiW) and weaning weight (WW), almost 3.4 million on postweaning gain (PWG), and over 1.3 million on calving ease (CE). Genomic information was available on, at most, 51,883 animals,which included high and low EBV accuracy animals. Traditional EBV was computed by BLUP and genomic EBV by ssGBLUP and indirect prediction based on SNP effects was derived from ssGBLUP; SNP effects were calculated based on the following reference populations: ref_2k (contains top bulls and top cows that had an EBV accuracy for BiW ≥0.85), ref_8k (contains all parents that were genotyped), and ref_33k (contains all genotyped animals born up to 2012). Indirect prediction was obtained as direct genomic value (DGV) or as anindex of DGV and parent average (PA). Additionally, runs with ssGBLUP used the inverse of the genomic relationship matrix calculated by an algorithm for proven and young animals (APY) that uses recursions on a small subset of reference animals. An extra reference subset included 3,872 genotyped parents of genotyped animals (ref_4k). Cross-validation was used to assess predictive ability on a validation population of 18,721 animals born in 2013. Computations for growth traits used multiple-trait linear model and, for CE, a bivariate CE?BiW threshold-linear model. With BLUP, predictivities were 0.29, 0.34, 0.23, and 0.12 for BiW, WW, PWG, and CE, respectively. With ssGBLUP and ref_2k, predictivities were 0.34, 0.35, 0.27, and 0.13 for BiW, WW, PWG, and CE, respectively, and with ssGBLUP and ref_33k, predictivities were 0.39, 0.38, 0.29, and 0.13 for BiW, WW, PWG, and CE, respectively. Low predictivity for CE was due to low incidence rate of difficult calving. Indirect predictions with ref_33k were as accurate as with full ssGBLUP. Using the APY and recursions on ref_4k gave 88% gains of full ssGBLUP and using the APY and recursions on ref_8k gave 97% gains of full ssGBLUP. Genomic evaluation in beef cattle with ssGBLUP is feasible while keeping the models (maternal, multiple trait, and threshold) already used in regular BLUP. Gains in predictivity are dependent on the composition of the reference population. Indirect predictions via SNP effects derived from ssGBLUP allow for accurate genomic predictions on young animals, with no advantage of including PA inthe index if the reference population is large. With the APY conditioning on about 10,000 reference animals, ssGBLUP is potentially applicable to a large number of genotyped animals without compromising predictive ability. © 2015 American Society of Animal Science. All rights reservedhttps://hdl.handle.net/20.500.12381/2469enenginfo:eu-repo/semantics/openAccessAcceso abiertoBEEF CATTLEGENETIC RESURSIONINDIRECT PREDICTIONGANADO DE CARNEMEJORAMIENTO GENETICO ANIMALGENOMIC SELECTIONGenetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaLOURENCO, D. A. L.TSURUTA, S.FRAGOMENI, B. O.MASUDA, Y.AGUILAR, I.LEGARRA, A.BERTRAND, J. K.AMEN, T. S.WANG. L.MOSER, D. W.MISZTAL, I.SWORDsword-2022-12-16T17:42:17.original.xmlOriginal SWORD entry documentapplication/octet-stream4298https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2469/1/sword-2022-12-16T17%3a42%3a17.original.xmld431b16ce6076d75252d724681bdb4e1MD5120.500.12381/24692022-12-16 17:42:18.429oai:redi.anii.org.uy:20.500.12381/2469Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-12-16T20:42:18AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
LOURENCO, D. A. L.
BEEF CATTLE
GENETIC RESURSION
INDIRECT PREDICTION
GANADO DE CARNE
MEJORAMIENTO GENETICO ANIMAL
GENOMIC SELECTION
status_str publishedVersion
title Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
title_full Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
title_fullStr Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
title_full_unstemmed Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
title_short Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
title_sort Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*)
topic BEEF CATTLE
GENETIC RESURSION
INDIRECT PREDICTION
GANADO DE CARNE
MEJORAMIENTO GENETICO ANIMAL
GENOMIC SELECTION
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=54005&biblioteca=vazio&busca=54005&qFacets=54005