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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Corte; Embrapa Gado de Leite. |
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Data corrente: |
23/12/2020 |
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Data da última atualização: |
06/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
PERIPOLLI, E.; REIMER, C.; HA, NGOC-THUY; GEIBEL. J.; MACHADO, M. A.; PANETTO, J. C. do C.; EGITO, A. A. do; BALDI, F.; SIMIANER, H.; SILVA, M. V. G. B. |
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Afiliação: |
Elisa Peripolli; Christian Reimer; Ngoc-Thuy Ha; Johannes Geibel; MARCO ANTONIO MACHADO, CNPGL; JOAO CLAUDIO DO CARMO PANETTO, CNPGL; ANDREA ALVES DO EGITO, CNPGC; Fernando Baldi; Henner Simianer; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
BMC Genomics, v. 21, article 624, 2020. |
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DOI: |
https://doi.org/10.1186/s12864-020-07035-6 |
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Idioma: |
Inglês |
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Conteúdo: |
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. MenosBackground: 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 cu... Mostrar Tudo |
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Palavras-Chave: |
Bos taurus indicus; Bos taurus taurus; Local adaptation; Next-generation sequencing; Signatures of selection. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1129869/1/Genome-wide-detection-of-signatures-of-selection-in-indicine-and-Brazilian.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/219647/1/34-Genome-wide.pdf
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Marc: |
LEADER 02861naa a2200301 a 4500
001 2129869
005 2024-02-06
008 2020 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1186/s12864-020-07035-6$2DOI
100 1 $aPERIPOLLI, E.
245 $aGenome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data.$h[electronic resource]
260 $c2020
520 $aBackground: 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.
653 $aBos taurus indicus
653 $aBos taurus taurus
653 $aLocal adaptation
653 $aNext-generation sequencing
653 $aSignatures of selection
700 1 $aREIMER, C.
700 1 $aHA, NGOC-THUY
700 1 $aGEIBEL. J.
700 1 $aMACHADO, M. A.
700 1 $aPANETTO, J. C. do C.
700 1 $aEGITO, A. A. do
700 1 $aBALDI, F.
700 1 $aSIMIANER, H.
700 1 $aSILVA, M. V. G. B.
773 $tBMC Genomics$gv. 21, article 624, 2020.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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| 1. |  | PERIPOLLI, E.; REIMER, C.; HA, NGOC-THUY; GEIBEL. J.; MACHADO, M. A.; PANETTO, J. C. do C.; EGITO, A. A. do; BALDI, F.; SIMIANER, H.; SILVA, M. V. G. B. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data. BMC Genomics, v. 21, article 624, 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Corte; Embrapa Gado de Leite. |
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| Registros recuperados : 1 | |
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