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Registro Completo |
Biblioteca(s): |
Embrapa Gado de Corte; Embrapa Gado de Leite. |
Data corrente: |
23/12/2020 |
Data da última atualização: |
06/02/2024 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
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. |
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. |
Título: |
Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data. |
Ano de publicação: |
2020 |
Fonte/Imprenta: |
BMC Genomics, v. 21, article 624, 2020. |
DOI: |
https://doi.org/10.1186/s12864-020-07035-6 |
Idioma: |
Inglês |
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 |
Palavras-Chave: |
Bos taurus indicus; Bos taurus taurus; Local adaptation; Next-generation sequencing; Signatures of selection. |
Categoria do assunto: |
-- |
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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Registros recuperados : 15 | |
2. | | PERIPOLLI, E.; MUNARI, D. P.; SILVA, M. V. G. B.; LIMA, A. L.; IRGANG, R.; BALDI, F. Runs of homozygosity: current knowledge and applications in livestock. Animal Genetics, v. 48, n. 3, p. 255-271, 2017. Publicado online em 1 dez. 2016.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
Biblioteca(s): Embrapa Gado de Leite. |
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3. | | PERIPOLLI, E.; STAFUZZA, N. B.; MACHADO, M. A.; PANETTO, J. C. do C.; EGITO, A. A. do; BALDI, F.; SILVA, M. V. G. B. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data. Animal Genetics, v. 54, n. 3, p. 254-270, 2023.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Gado de Leite. |
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4. | | PERIPOLLI, E.; OLIVIERI, B. F.; BERTON, M. P.; MUNARI, D. P.; SILVA, M. V. G. B.; B. FERNANDO; FEITOSA, F. L. B. Imbreeding estimates using two different approaches in Gry cattle In: INTERNATIONAL MEETING OF ADVANCES IN ANIMAL SCIENCE, 1., 2016, Jaboticabal. Anais ... Jaboticabal: [S.N.], 2016.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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5. | | PERIPOLLI, E.; TONUSSI, R. L; VERNEQUE, R. Da S.; PANETTO, J. C. do C.; MACHADO, M. A.; SILVA, M. V. G. B.; BALDI, F. Exploring runs of homozygosity patterns in Gyr cattle. In: INTERNATIONAL MEETING OF ADVANCES IN ANIMAL SCIENCE, 1, 2016, Jaboticabal. Anais ... Jaboticabal: [s.n.], 2016.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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6. | | PERIPOLLI, E.; STAFUZZA, N. B.; MUNARI, D. P.; LIMA, A. L. F.; IRGANG, R.; MACHADO, M. A.; PANETTO, J. C. do C.; VENTURA, R. V.; BALDI, F.; SILVA, M. V. G. B. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics, v. 19, n. 34, 2018. 13 p.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Gado de Leite. |
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7. | | PERIPOLLI, E.; OLIVIERI. B. F.; FEITOSA, F. L. B.; LEMOS, M. V. A. de; TONUSSI, R. L.; MUNARI, D. P.; PANETTO, J. C. do C.; MACHADO, M. A.; VENTURA, R. V.; BALDI, F.; SILVA, M. V. G. B. Avaliação dos coeficientes de endogamia em bovinos da raça Gir (Bos primigenius indicus) In: SIMPÓSIO BRASILEIRO DE MELHORAMENTO ANIMAL, 12., 2017, Ribeirão Preto. Anais... Ribeirão Preto: SBMA, 2017. 3 p.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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8. | | PERIPOLLI, E.; CHIAIA, H. L. J.; BERTON, M. P.; KLUSKA, S.; STAFUZZA, N. B.; MUNARI, D. P.; PANETTO, J. C. do C.; MACHADO, M. A.; VENTURA, R. V.; BALDI, F.; SILVA, M. V. G. B. Ilhas de homozigose para identificação de genes relacionados com características de importância econômica na pecuária leiteira em bovinos da raça Gir (Bos primigenius indicus) In: SIMPÓSIO BRASILEIRO DE MELHORAMENTO ANIMAL, 12., 2017, Ribeirão Preto. Anais... Ribeirão Preto: SBMA, 2017. 3 p.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Gado de Leite. |
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9. | | STAFUZZA, N. B.; SILVA, R. M. de O.; PERIPOLLI, E.; BEZERRA, L. A. F.; LOBO, R. B.; MAGNABOSCO, C. de U.; DI CROCE, F.; OSTERSTOCK, J.; MUNARI, D. P.; LOURENCO, D. A. L.; BALDI, F. Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle. PLoS ONE, v. 13, n. 8, e0202978, August 30, 2018.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Cerrados. |
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10. | | 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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11. | | TONUSSI, R. L.; SILVA, R. M. de O.; MAGALHAES, A. F. B.; ESPIGOLAN, R.; PERIPOLLI, E.; OLIVIERI, B. F.; FEITOSA, F. L. B.; LEMOS, M. V. A.; BERTON, M. P.; CHIAIA, H. L. J.; PEREIRA, A. S. C.; LOBO, R. B.; BEZERRA, L. A. F.; MAGNABOSCO, C. de U.; LOURENÇO, D. A. L.; AGUILAR, I.; BALDI REY, F. S. Application of single step genomic BLUP under different uncertain paternity scenarios using simulated data. PLoS ONE, v. 12, n. 9, e0181752, 28 September 2017.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Cerrados. |
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12. | | PERIPOLLI, E.; METZGER, J.; LEMOS, M. V. A. de; STAFUZZA, N. B.; KLUSKA, S.; OLIVIERI, B. F.; FEITOSA, F. L. B.; BERTON, M. P.; LOPES, F. B.; MUNARI, D. P.; LOBO, R. B.; MAGNABOSCO, C. de U.; DI CROCE, F.; OSTERSTOCK, J.; DENISE, S.; PEREIRA, A. S. C.; BALDI, F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics, v. 19, 680, 2018.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Cerrados. |
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13. | | KLUSKA, S.; TONUSSI, R. L.; SILVA, R. M. de O.; OLIVERI, B. F.; FEITOSA, F. L. B.; PERIPOLLI, E.; LEMOS, M. V. A.; BERTON, M. P.; CHIAIA, H. L. J.; PEREIRA, A. S. C.; LOBO, R. B.; BEZERRA, L. A.; MAGNABOSCO, C. de U.; AGUILAR, I.; DI CROCE, F.; OSTERSTOCK, J.; BALDI REY, F. S. Caracterização do desequilíbrio de ligação em uma população de bovinos da raça Nelore. In: SIMPÓSIO BRASILEIRO DE MELHORAMENTO ANIMAL, 12., 2017, Ribeirão Preto, SP. Fenômica e outras ômicas na produção animal: anais... Sertãozinho: Sociedade de Melhoramento Animal/Instituto de Zootecnia, 2017. SBMA 2017. 3 p.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Cerrados. |
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14. | | TONUSSI, R. L.; SILVA, R. M. de O.; OLIVERI, B. F.; FEITOSA, F. L. B.; PERIPOLLI, E.; LEMOS, M. V. A.; BERTON, M. P.; PEREIRA, A. S. C.; LOBO, R. B.; BEZERRA, L. A. F.; MAGNABOSCO, C. de U.; AGUILAR, I.; DI CROCE, F. A.; BALDI REY, F. S. Impacto nas acurácias dos valores genéticos para idade ao primeiro parto em diferentes cenários com paternidade incerta. In: SIMPÓSIO BRASILEIRO DE MELHORAMENTO ANIMAL, 12., 2017, Ribeirão Preto, SP. Fenômica e outras ômicas na produção animal: anais... Sertãozinho: Sociedade de Melhoramento Animal/Instituto de Zootecnia, 2017. SBMA 2017. 4 p.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Cerrados. |
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15. | | KLUSKA, S.; OLIVIERI, B. F.; BONAMY, M.; CHIAIA, H. L. J.; FEITOSA, F. L. B.; BERTON, M. P.; PERIPOLLI, E.; LEMOS, M. V. A.; TONUSSI, R. L.; LOBO, R. B.; MAGNABOSCO, C. de U.; CI CROCE, F.; OSTERSTOCK, J.; PEREIRA, A. S. C.; MUNARI, D. P.; BEZERRA, L. A.; LOPES, F. B.; BALDI, F. Estimates of genetic parameters for growth, reproductive, and carcass traits in Nelore cattle using the single step genomic BLUP procedure. Livestock Science, v. 216, p. 203-209, October 2018.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
Biblioteca(s): Embrapa Cerrados. |
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Registros recuperados : 15 | |
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Nenhum registro encontrado para a expressão de busca informada. |
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