Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s12711-018-0381-2 http://hdl.handle.net/11449/166122 |
Resumo: | Background: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results: Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (F-ST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions: The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. |
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spelling |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattleBackground: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results: Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (F-ST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions: The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Sao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, BrazilNatl Counsel Technol & Sci Dev CNPq, Brasilia, DF, BrazilUniv Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, GermanyBavarian State Res Ctr Agr, Inst Anim Breeding, Grub, GermanyAPTA Beef Cattle Ctr, Inst Anim Sci, Sertaozinho, SP, BrazilSao Paulo State Univ, Fac Agr & Vet Sci, Dept Anim Sci, Jaboticabal, SP, BrazilFAPESP: 2009/16118-5: 2012/24600-4: 2014/13445-3Biomed Central LtdUniversidade Estadual Paulista (Unesp)Natl Counsel Technol & Sci Dev CNPqUniv GoettingenBavarian State Res Ctr AgrAPTA Beef Cattle CtrCardoso, Diercles F. [UNESP]Albuquerque, Lucia Galvao de [UNESP]Reimer, ChristianQanbari, SaberErbe, MalenaNascimento, Andre V. do [UNESP]Venturini, Guilherme C. [UNESP]Becker Scalez, Daiane C. [UNESP]Baldi, Fernando [UNESP]Ferreira de Camargo, Gregorio M. [UNESP]Zerlotti Mercadante, Maria E.Santos Goncalves Cyrillo, Joslaine N. doSimianer, HennerTonhati, Humberto [UNESP]2018-11-29T13:28:33Z2018-11-29T13:28:33Z2018-05-02info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://dx.doi.org/10.1186/s12711-018-0381-2Genetics Selection Evolution. London: Biomed Central Ltd, v. 50, 12 p., 2018.0999-193Xhttp://hdl.handle.net/11449/16612210.1186/s12711-018-0381-2WOS:000431616500002WOS000431616500002.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenetics Selection Evolutioninfo:eu-repo/semantics/openAccess2024-06-07T18:40:52Zoai:repositorio.unesp.br:11449/166122Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-06-07T18:40:52Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
title |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
spellingShingle |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle Cardoso, Diercles F. [UNESP] |
title_short |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
title_full |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
title_fullStr |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
title_full_unstemmed |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
title_sort |
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle |
author |
Cardoso, Diercles F. [UNESP] |
author_facet |
Cardoso, Diercles F. [UNESP] Albuquerque, Lucia Galvao de [UNESP] Reimer, Christian Qanbari, Saber Erbe, Malena Nascimento, Andre V. do [UNESP] Venturini, Guilherme C. [UNESP] Becker Scalez, Daiane C. [UNESP] Baldi, Fernando [UNESP] Ferreira de Camargo, Gregorio M. [UNESP] Zerlotti Mercadante, Maria E. Santos Goncalves Cyrillo, Joslaine N. do Simianer, Henner Tonhati, Humberto [UNESP] |
author_role |
author |
author2 |
Albuquerque, Lucia Galvao de [UNESP] Reimer, Christian Qanbari, Saber Erbe, Malena Nascimento, Andre V. do [UNESP] Venturini, Guilherme C. [UNESP] Becker Scalez, Daiane C. [UNESP] Baldi, Fernando [UNESP] Ferreira de Camargo, Gregorio M. [UNESP] Zerlotti Mercadante, Maria E. Santos Goncalves Cyrillo, Joslaine N. do Simianer, Henner Tonhati, Humberto [UNESP] |
author2_role |
author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Natl Counsel Technol & Sci Dev CNPq Univ Goettingen Bavarian State Res Ctr Agr APTA Beef Cattle Ctr |
dc.contributor.author.fl_str_mv |
Cardoso, Diercles F. [UNESP] Albuquerque, Lucia Galvao de [UNESP] Reimer, Christian Qanbari, Saber Erbe, Malena Nascimento, Andre V. do [UNESP] Venturini, Guilherme C. [UNESP] Becker Scalez, Daiane C. [UNESP] Baldi, Fernando [UNESP] Ferreira de Camargo, Gregorio M. [UNESP] Zerlotti Mercadante, Maria E. Santos Goncalves Cyrillo, Joslaine N. do Simianer, Henner Tonhati, Humberto [UNESP] |
description |
Background: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results: Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (F-ST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions: The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-29T13:28:33Z 2018-11-29T13:28:33Z 2018-05-02 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/s12711-018-0381-2 Genetics Selection Evolution. London: Biomed Central Ltd, v. 50, 12 p., 2018. 0999-193X http://hdl.handle.net/11449/166122 10.1186/s12711-018-0381-2 WOS:000431616500002 WOS000431616500002.pdf |
url |
http://dx.doi.org/10.1186/s12711-018-0381-2 http://hdl.handle.net/11449/166122 |
identifier_str_mv |
Genetics Selection Evolution. London: Biomed Central Ltd, v. 50, 12 p., 2018. 0999-193X 10.1186/s12711-018-0381-2 WOS:000431616500002 WOS000431616500002.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genetics Selection Evolution |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
12 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd |
publisher.none.fl_str_mv |
Biomed Central Ltd |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803045301221588992 |