Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.

MOTA, R. R. - LOPES, P. S. - TEMPELMAN, R. J. - SILVA, F. F. - AGUILAR, I. - GOMES, C. C. G. - CARDOSO, F. F.

Resumen:

ABSTRACT.Very few studies have been conducted to infer genotype × environment interaction (G×E) based in genomic prediction models using SNP markers. Therefore, our main objective was to compare a conventional genomic-based single-step model (HBLUP) with its reaction norm model extension (genomic 1-step linear reaction norm model [HLRNM]) to provide EBV for tick resistance as well as to compare predictive performance of these models with counterpart models that ignore SNP marker information, that is, a linear animal model (ABLUP) and its reaction norm extension (1-step linear reaction norm model [ALRNM]). Phenotypes included 10,673 tick counts on 4,363 Hereford and Braford animals, of which 3,591 were genotyped. Using the deviance information criterion for model choice, ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic model extensions. The HLRNM estimated lower average and reaction norm genetic variability compared with the ALRNM, whereas ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic reaction norm model extensions. Heritability and repeatability estimates varied along the environmental gradient (EG) and the genetic correlations were remarkably low between high and low EG, indicating the presence of G×E for tick resistance in these populations. Based on 5-fold K-means partitioning, mean cross-validation estimates with their respective SE of predictive accuracy were 0.66 (SE 0.02), 0.67 (SE 0.02), 0.67 (SE 0.02), and 0.66 (SE 0.02) for ABLUP, HBLUP, HLRNM, and ALRNM, respectively. For 5-fold random partitioning, HLRNM (0.71 ± 0.01) was statistically different from ABLUP (0.67 ± 0.01). However, no statistical significance was reported when considering HBLUP (0.70 ± 0.01) and ALRNM (0.70 ± 0.01). Our results suggest that SNP marker information does not lead to higher prediction accuracies in reaction norm models. Furthermore, these accuracies decreased as the tick infestation level increased and as the relationship between animals in training and validation data sets decreased. © 2016 American Society of Animal Science. All rights reserved.


Detalles Bibliográficos
2016
ACCURACY
CROSS-VALIDATION
GENETIC CORRELATION
HERITABILITY
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=59370&biblioteca=vazio&busca=59370&qFacets=59370
Acceso abierto
_version_ 1805580526447230976
author MOTA, R. R.
author2 LOPES, P. S.
TEMPELMAN, R. J.
SILVA, F. F.
AGUILAR, I.
GOMES, C. C. G.
CARDOSO, F. F.
author2_role author
author
author
author
author
author
author_facet MOTA, R. R.
LOPES, P. S.
TEMPELMAN, R. J.
SILVA, F. F.
AGUILAR, I.
GOMES, C. C. G.
CARDOSO, F. F.
author_role author
bitstream.checksum.fl_str_mv 6f4fbe34c717e370c3ebcdbc521367fe
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3111/1/sword-2022-12-16T18%3a06%3a36.original.xml
collection AINFO
dc.creator.none.fl_str_mv MOTA, R. R.
LOPES, P. S.
TEMPELMAN, R. J.
SILVA, F. F.
AGUILAR, I.
GOMES, C. C. G.
CARDOSO, F. F.
dc.date.accessioned.none.fl_str_mv 2022-12-16T21:06:36Z
dc.date.available.none.fl_str_mv 2022-12-16T21:06:36Z
dc.date.issued.none.fl_str_mv 2016
dc.date.updated.none.fl_str_mv 2022-12-16T21:06:36Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.Very few studies have been conducted to infer genotype × environment interaction (G×E) based in genomic prediction models using SNP markers. Therefore, our main objective was to compare a conventional genomic-based single-step model (HBLUP) with its reaction norm model extension (genomic 1-step linear reaction norm model [HLRNM]) to provide EBV for tick resistance as well as to compare predictive performance of these models with counterpart models that ignore SNP marker information, that is, a linear animal model (ABLUP) and its reaction norm extension (1-step linear reaction norm model [ALRNM]). Phenotypes included 10,673 tick counts on 4,363 Hereford and Braford animals, of which 3,591 were genotyped. Using the deviance information criterion for model choice, ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic model extensions. The HLRNM estimated lower average and reaction norm genetic variability compared with the ALRNM, whereas ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic reaction norm model extensions. Heritability and repeatability estimates varied along the environmental gradient (EG) and the genetic correlations were remarkably low between high and low EG, indicating the presence of G×E for tick resistance in these populations. Based on 5-fold K-means partitioning, mean cross-validation estimates with their respective SE of predictive accuracy were 0.66 (SE 0.02), 0.67 (SE 0.02), 0.67 (SE 0.02), and 0.66 (SE 0.02) for ABLUP, HBLUP, HLRNM, and ALRNM, respectively. For 5-fold random partitioning, HLRNM (0.71 ± 0.01) was statistically different from ABLUP (0.67 ± 0.01). However, no statistical significance was reported when considering HBLUP (0.70 ± 0.01) and ALRNM (0.70 ± 0.01). Our results suggest that SNP marker information does not lead to higher prediction accuracies in reaction norm models. Furthermore, these accuracies decreased as the tick infestation level increased and as the relationship between animals in training and validation data sets decreased. © 2016 American Society of Animal Science. All rights reserved.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=59370&biblioteca=vazio&busca=59370&qFacets=59370
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 ACCURACY
CROSS-VALIDATION
GENETIC CORRELATION
HERITABILITY
dc.title.none.fl_str_mv Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
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.Very few studies have been conducted to infer genotype × environment interaction (G×E) based in genomic prediction models using SNP markers. Therefore, our main objective was to compare a conventional genomic-based single-step model (HBLUP) with its reaction norm model extension (genomic 1-step linear reaction norm model [HLRNM]) to provide EBV for tick resistance as well as to compare predictive performance of these models with counterpart models that ignore SNP marker information, that is, a linear animal model (ABLUP) and its reaction norm extension (1-step linear reaction norm model [ALRNM]). Phenotypes included 10,673 tick counts on 4,363 Hereford and Braford animals, of which 3,591 were genotyped. Using the deviance information criterion for model choice, ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic model extensions. The HLRNM estimated lower average and reaction norm genetic variability compared with the ALRNM, whereas ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic reaction norm model extensions. Heritability and repeatability estimates varied along the environmental gradient (EG) and the genetic correlations were remarkably low between high and low EG, indicating the presence of G×E for tick resistance in these populations. Based on 5-fold K-means partitioning, mean cross-validation estimates with their respective SE of predictive accuracy were 0.66 (SE 0.02), 0.67 (SE 0.02), 0.67 (SE 0.02), and 0.66 (SE 0.02) for ABLUP, HBLUP, HLRNM, and ALRNM, respectively. For 5-fold random partitioning, HLRNM (0.71 ± 0.01) was statistically different from ABLUP (0.67 ± 0.01). However, no statistical significance was reported when considering HBLUP (0.70 ± 0.01) and ALRNM (0.70 ± 0.01). Our results suggest that SNP marker information does not lead to higher prediction accuracies in reaction norm models. Furthermore, these accuracies decreased as the tick infestation level increased and as the relationship between animals in training and validation data sets decreased. © 2016 American Society of Animal Science. All rights reserved.
eu_rights_str_mv openAccess
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spelling 2022-12-16T21:06:36Z2022-12-16T21:06:36Z20162022-12-16T21:06:36Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=59370&biblioteca=vazio&busca=59370&qFacets=59370ABSTRACT.Very few studies have been conducted to infer genotype × environment interaction (G×E) based in genomic prediction models using SNP markers. Therefore, our main objective was to compare a conventional genomic-based single-step model (HBLUP) with its reaction norm model extension (genomic 1-step linear reaction norm model [HLRNM]) to provide EBV for tick resistance as well as to compare predictive performance of these models with counterpart models that ignore SNP marker information, that is, a linear animal model (ABLUP) and its reaction norm extension (1-step linear reaction norm model [ALRNM]). Phenotypes included 10,673 tick counts on 4,363 Hereford and Braford animals, of which 3,591 were genotyped. Using the deviance information criterion for model choice, ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic model extensions. The HLRNM estimated lower average and reaction norm genetic variability compared with the ALRNM, whereas ABLUP and HBLUP seemed to be poorer fitting in comparison with their respective genomic reaction norm model extensions. Heritability and repeatability estimates varied along the environmental gradient (EG) and the genetic correlations were remarkably low between high and low EG, indicating the presence of G×E for tick resistance in these populations. Based on 5-fold K-means partitioning, mean cross-validation estimates with their respective SE of predictive accuracy were 0.66 (SE 0.02), 0.67 (SE 0.02), 0.67 (SE 0.02), and 0.66 (SE 0.02) for ABLUP, HBLUP, HLRNM, and ALRNM, respectively. For 5-fold random partitioning, HLRNM (0.71 ± 0.01) was statistically different from ABLUP (0.67 ± 0.01). However, no statistical significance was reported when considering HBLUP (0.70 ± 0.01) and ALRNM (0.70 ± 0.01). Our results suggest that SNP marker information does not lead to higher prediction accuracies in reaction norm models. Furthermore, these accuracies decreased as the tick infestation level increased and as the relationship between animals in training and validation data sets decreased. © 2016 American Society of Animal Science. All rights reserved.https://hdl.handle.net/20.500.12381/3111enenginfo:eu-repo/semantics/openAccessAcceso abiertoACCURACYCROSS-VALIDATIONGENETIC CORRELATIONHERITABILITYGenome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaMOTA, R. R.LOPES, P. S.TEMPELMAN, R. J.SILVA, F. F.AGUILAR, I.GOMES, C. C. G.CARDOSO, F. F.SWORDsword-2022-12-16T18:06:36.original.xmlOriginal SWORD entry documentapplication/octet-stream3393https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3111/1/sword-2022-12-16T18%3a06%3a36.original.xml6f4fbe34c717e370c3ebcdbc521367feMD5120.500.12381/31112022-12-16 18:06:37.159oai:redi.anii.org.uy:20.500.12381/3111Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-12-16T21:06:37AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
MOTA, R. R.
ACCURACY
CROSS-VALIDATION
GENETIC CORRELATION
HERITABILITY
status_str publishedVersion
title Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
title_full Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
title_fullStr Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
title_full_unstemmed Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
title_short Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
title_sort Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models.
topic ACCURACY
CROSS-VALIDATION
GENETIC CORRELATION
HERITABILITY
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=59370&biblioteca=vazio&busca=59370&qFacets=59370