Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.

Detalhes bibliográficos
Autor(a) principal: CARDOSO, D. F.
Data de Publicação: 2020
Outros Autores: FERNANDES JÚNIOR, G. A., SCALEZ, D. C. B., ALVEZ, A. A. C., MAGALHÃES, A. F. B., BRESOLIN, T., VENTURA, R. V., LI, C., OLIVEIRA, M. C. de S., PORTO NETO, L. R., CARVALHEIRO, R., OLIVEIRA, H. N. de, TONHATI, H., ALBUQUERQUE, L. G.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1127803
https://doi.org/10.1038/s41598-020-65565-1
Resumo: Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N?= 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77?65.25 Mb) and 14 (22.81?23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.
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spelling Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.Autozygosity islandsRather similar acrossOverall genomic diversityROH islandsFSTVarLD signalsAngusHighlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N?= 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77?65.25 Mb) and 14 (22.81?23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.Diercles Francisco Cardoso, UNESP; Gerardo Alves Fernandes Júnior, UNESP; Daiane Cristina Becker Scalez, UNESP; Anderson Antonio Carvalho Alves, UNESP; Ana Fabrícia Braga Magalhães, UNESP; Tiago Bresolin, UNESP; Ricardo Vieira Ventura, USP; Changxi Li, University of Alberta; MARCIA CRISTINA DE SENA OLIVEIRA, CPPSE; Laercio Ribeiro Porto-Neto, CSIRO; Roberto Carvalheiro, UNESP; Henrique Nunes de Oliveira, UNESP; Humberto Tonhati, UNESP; Lucia Galvão Albuquerque, UNESP.CARDOSO, D. F.FERNANDES JÚNIOR, G. A.SCALEZ, D. C. B.ALVEZ, A. A. C.MAGALHÃES, A. F. B.BRESOLIN, T.VENTURA, R. V.LI, C.OLIVEIRA, M. C. de S.PORTO NETO, L. R.CARVALHEIRO, R.OLIVEIRA, H. N. deTONHATI, H.ALBUQUERQUE, L. G.2020-12-09T09:07:24Z2020-12-09T09:07:24Z2020-12-082020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article11 p.Scientific Reports, v. 10, article 8770, 2020.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1127803https://doi.org/10.1038/s41598-020-65565-1enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2020-12-09T09:07:32Zoai:www.alice.cnptia.embrapa.br:doc/1127803Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542020-12-09T09:07:32falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542020-12-09T09:07:32Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
title Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
spellingShingle Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
CARDOSO, D. F.
Autozygosity islands
Rather similar across
Overall genomic diversity
ROH islands
FST
VarLD signals
Angus
title_short Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
title_full Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
title_fullStr Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
title_full_unstemmed Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
title_sort Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle.
author CARDOSO, D. F.
author_facet CARDOSO, D. F.
FERNANDES JÚNIOR, G. A.
SCALEZ, D. C. B.
ALVEZ, A. A. C.
MAGALHÃES, A. F. B.
BRESOLIN, T.
VENTURA, R. V.
LI, C.
OLIVEIRA, M. C. de S.
PORTO NETO, L. R.
CARVALHEIRO, R.
OLIVEIRA, H. N. de
TONHATI, H.
ALBUQUERQUE, L. G.
author_role author
author2 FERNANDES JÚNIOR, G. A.
SCALEZ, D. C. B.
ALVEZ, A. A. C.
MAGALHÃES, A. F. B.
BRESOLIN, T.
VENTURA, R. V.
LI, C.
OLIVEIRA, M. C. de S.
PORTO NETO, L. R.
CARVALHEIRO, R.
OLIVEIRA, H. N. de
TONHATI, H.
ALBUQUERQUE, L. G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Diercles Francisco Cardoso, UNESP; Gerardo Alves Fernandes Júnior, UNESP; Daiane Cristina Becker Scalez, UNESP; Anderson Antonio Carvalho Alves, UNESP; Ana Fabrícia Braga Magalhães, UNESP; Tiago Bresolin, UNESP; Ricardo Vieira Ventura, USP; Changxi Li, University of Alberta; MARCIA CRISTINA DE SENA OLIVEIRA, CPPSE; Laercio Ribeiro Porto-Neto, CSIRO; Roberto Carvalheiro, UNESP; Henrique Nunes de Oliveira, UNESP; Humberto Tonhati, UNESP; Lucia Galvão Albuquerque, UNESP.
dc.contributor.author.fl_str_mv CARDOSO, D. F.
FERNANDES JÚNIOR, G. A.
SCALEZ, D. C. B.
ALVEZ, A. A. C.
MAGALHÃES, A. F. B.
BRESOLIN, T.
VENTURA, R. V.
LI, C.
OLIVEIRA, M. C. de S.
PORTO NETO, L. R.
CARVALHEIRO, R.
OLIVEIRA, H. N. de
TONHATI, H.
ALBUQUERQUE, L. G.
dc.subject.por.fl_str_mv Autozygosity islands
Rather similar across
Overall genomic diversity
ROH islands
FST
VarLD signals
Angus
topic Autozygosity islands
Rather similar across
Overall genomic diversity
ROH islands
FST
VarLD signals
Angus
description Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N?= 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77?65.25 Mb) and 14 (22.81?23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.
publishDate 2020
dc.date.none.fl_str_mv 2020-12-09T09:07:24Z
2020-12-09T09:07:24Z
2020-12-08
2020
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv Scientific Reports, v. 10, article 8770, 2020.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1127803
https://doi.org/10.1038/s41598-020-65565-1
identifier_str_mv Scientific Reports, v. 10, article 8770, 2020.
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1127803
https://doi.org/10.1038/s41598-020-65565-1
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 11 p.
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
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