Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

Detalhes bibliográficos
Autor(a) principal: Peripolli, Elisa [UNESP]
Data de Publicação: 2020
Outros Autores: Reimer, Christian, Ha, Ngoc-Thuy, Geibel, Johannes, Machado, Marco Antonio, Panetto, João Cláudio do Carmo, do Egito, Andréa Alves, Baldi, Fernando [UNESP], Simianer, Henner, da Silva, Marcos Vinícius Gualberto Barbosa
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/s12864-020-07035-6
http://hdl.handle.net/11449/199392
Resumo: BACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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spelling Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing dataBos taurus indicusBos taurus taurusLocal adaptationNext-generation sequencingSignatures of selectionBACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)São Paulo State University (Unesp) School of Agricultural and Veterinarian SciencesAnimal Breeding and Genetics Group Department of Animal Sciences University of Goettingen, Albrecht-Thaer-Weg 3Center for Integrated Breeding Research University of Goettingen, Albrecht-Thaer-Weg 3National Council for Scientific and Technological Development (CNPq)Embrapa Dairy CattleEmbrapa Beef CattleSão Paulo State University (Unesp) School of Agricultural and Veterinarian SciencesUniversidade Estadual Paulista (Unesp)University of GoettingenNational Council for Scientific and Technological Development (CNPq)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Peripolli, Elisa [UNESP]Reimer, ChristianHa, Ngoc-ThuyGeibel, JohannesMachado, Marco AntonioPanetto, João Cláudio do Carmodo Egito, Andréa AlvesBaldi, Fernando [UNESP]Simianer, Hennerda Silva, Marcos Vinícius Gualberto Barbosa2020-12-12T01:38:31Z2020-12-12T01:38:31Z2020-09-11info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article624http://dx.doi.org/10.1186/s12864-020-07035-6BMC genomics, v. 21, n. 1, p. 624-, 2020.1471-2164http://hdl.handle.net/11449/19939210.1186/s12864-020-07035-62-s2.0-85090897517Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC genomicsinfo:eu-repo/semantics/openAccess2021-10-22T20:18:54Zoai:repositorio.unesp.br:11449/199392Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:10:49.053658Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
spellingShingle Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
Peripolli, Elisa [UNESP]
Bos taurus indicus
Bos taurus taurus
Local adaptation
Next-generation sequencing
Signatures of selection
title_short Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_full Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_fullStr Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_full_unstemmed Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_sort Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
author Peripolli, Elisa [UNESP]
author_facet Peripolli, Elisa [UNESP]
Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando [UNESP]
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
author_role author
author2 Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando [UNESP]
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
University of Goettingen
National Council for Scientific and Technological Development (CNPq)
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.contributor.author.fl_str_mv Peripolli, Elisa [UNESP]
Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando [UNESP]
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
dc.subject.por.fl_str_mv Bos taurus indicus
Bos taurus taurus
Local adaptation
Next-generation sequencing
Signatures of selection
topic Bos taurus indicus
Bos taurus taurus
Local adaptation
Next-generation sequencing
Signatures of selection
description BACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
publishDate 2020
dc.date.none.fl_str_mv 2020-12-12T01:38:31Z
2020-12-12T01:38:31Z
2020-09-11
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/s12864-020-07035-6
BMC genomics, v. 21, n. 1, p. 624-, 2020.
1471-2164
http://hdl.handle.net/11449/199392
10.1186/s12864-020-07035-6
2-s2.0-85090897517
url http://dx.doi.org/10.1186/s12864-020-07035-6
http://hdl.handle.net/11449/199392
identifier_str_mv BMC genomics, v. 21, n. 1, p. 624-, 2020.
1471-2164
10.1186/s12864-020-07035-6
2-s2.0-85090897517
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC genomics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 624
dc.source.none.fl_str_mv Scopus
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
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