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 | Acesso ao texto completo restrito à biblioteca da Embrapa Suínos e Aves. Para informações adicionais entre em contato com cnpsa.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Suínos e Aves. |
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Data corrente: |
04/11/2019 |
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Data da última atualização: |
04/11/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
ALMEIDA, O. A. C.; MOREIRA, G. C. M.; REZENDE, F. M.; BOSCHIERO, C.; PEIXOTO, J. de O.; IBELLI, A. M. G.; LEDUR, M. C.; NOVAIS, F. J. de; COUTINHO, L. L. |
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Afiliação: |
OCTÁVIO AUGUSTO COSTA ALMEIDA, ESALQ; GABRIEL COSTA MONTEIRO MOREIRA, ESALQ; FERNANDA MARCONDES REZENDE, ESALQ; CLARISSA BOSCHIERO, ESALQ; JANE DE OLIVEIRA PEIXOTO, CNPSA; ADRIANA MERCIA GUARATINI IBELLI, CNPSA; MONICA CORREA LEDUR, CNPSA; FRANCISCO JOSÉ DE NOVAIS, ESALQ; LUIZ LEHMANN COUTINHO, ESALQ. |
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Título: |
Identification of selection signatures involved in performance traits in a paternal broiler line. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
BMC Genomics, v. 20, n. 449, 2019. |
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DOI: |
10.1186/s12864-019-5811-1 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract: Background: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-bydescent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. Results: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FSTbased analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. Conclusions: Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits. MenosAbstract: Background: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-bydescent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. Results: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FSTbased analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associa... Mostrar Tudo |
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Palavras-Chave: |
Fixation index; FST; Runs of homozygosity. |
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Thesagro: |
Galinha; Genética Molecular; Genoma; Linhagem; Melhoramento Genético Animal; Seleção Genótipa. |
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Thesaurus Nal: |
Artificial selection; Chickens; Gallus gallus. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03218naa a2200373 a 4500
001 2113872
005 2019-11-04
008 2019 bl uuuu u00u1 u #d
024 7 $a10.1186/s12864-019-5811-1$2DOI
100 1 $aALMEIDA, O. A. C.
245 $aIdentification of selection signatures involved in performance traits in a paternal broiler line.$h[electronic resource]
260 $c2019
520 $aAbstract: Background: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-bydescent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. Results: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FSTbased analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. Conclusions: Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.
650 $aArtificial selection
650 $aChickens
650 $aGallus gallus
650 $aGalinha
650 $aGenética Molecular
650 $aGenoma
650 $aLinhagem
650 $aMelhoramento Genético Animal
650 $aSeleção Genótipa
653 $aFixation index
653 $aFST
653 $aRuns of homozygosity
700 1 $aMOREIRA, G. C. M.
700 1 $aREZENDE, F. M.
700 1 $aBOSCHIERO, C.
700 1 $aPEIXOTO, J. de O.
700 1 $aIBELLI, A. M. G.
700 1 $aLEDUR, M. C.
700 1 $aNOVAIS, F. J. de
700 1 $aCOUTINHO, L. L.
773 $tBMC Genomics$gv. 20, n. 449, 2019.
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Embrapa Suínos e Aves (CNPSA) |
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| 1. |  | TRZRCIAK, M. B.; NEVES, M. B.; VINHOLES, P. S.; PERES, W. B.; VERNETTI JUNIOR, F. de J.; VILLELA, F. A. Adaptação de cultivares de soja: coeficientes de rendimento, produtividade e qualidade de sementes. In: CONGRESSO BRASILEIRO DE SEMENTES, 17., 2011, Natal. [Resumos.]. Informativo ABRATES, Londrina, v. 21, n. 2, ago. 2011.| Tipo: Resumo em Anais de Congresso |
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