Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , |
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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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 |
|
_version_ |
1808128614769623040 |