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Registro Completo |
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Biblioteca(s): |
Embrapa Suínos e Aves. |
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Data corrente: |
03/08/2021 |
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Data da última atualização: |
03/08/2021 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
FERNANDES, A. C.; SILVA, V. H. da; GOES, C. P.; MOREIRA, G. C. M.; GODOY, T. F.; IBELLI, A. M. G.; PEIXOTO, J. de O.; CANTAO, M. E.; LEDUR, M. C.; REZENDE, F. M. de; COUTINHO, L. L. |
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Afiliação: |
ANNA CAROLINA FERNANDES, ESALQ; VINICIUS HENRIQUE DA SILVA, ESALQ; CAROLINA PURCELL GOES, ESALQ; GABRIEL COSTA MONTEIRO MOREIRA, University of Liège; THAIS FERNANDA GODOY, ESALQ; ADRIANA MERCIA GUARATINI IBELLI, CNPSA; JANE DE OLIVEIRA PEIXOTO, CNPSA; MAURICIO EGIDIO CANTAO, CNPSA; MONICA CORREA LEDUR, CNPSA; FERNANDA MARCONDES REZENDE, University of Florida; LUIZ LEHMANN COUTINHO, ESALQ. |
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Título: |
Genome-wide detection of CNVs and their association with performance traits in broilers. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
BMC Genomics, v. 22, n. 354, 2021. |
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DOI: |
https://doi.org/10.1186/s12864-021-07676-1 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract
Background: Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic
architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We
identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide
CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated
into segments and association analyses were performed with linear mixed models considering a genomic
relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed
conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.
Results: We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of
the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value =
0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and
BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value =
0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These
CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and
development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes
regulation and potassium channels.
Conclusions: Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate
performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific
genes in regulating performance in chickens.
Keywords: GWAS, Performance, CNVs, QTLs, qPCR MenosAbstract
Background: Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic
architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We
identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide
CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated
into segments and association analyses were performed with linear mixed models considering a genomic
relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed
conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.
Results: We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of
the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value =
0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and
BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value =
0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These
CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and
development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular p... Mostrar Tudo |
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Palavras-Chave: |
CNVs; Copy number variations; Desempenho zootécnico; GWAS; QPCR; QTLs. |
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Thesagro: |
Gallus Domesticus; Genética Animal; Performance. |
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Thesaurus Nal: |
Animal genetics; Animal performance; Gallus gallus; Genome-wide association study; Quantitative polymerase chain reaction; Quantitative trait loci. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/224781/1/final9547.pdf
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Marc: |
LEADER 03101naa a2200433 a 4500
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024 7 $ahttps://doi.org/10.1186/s12864-021-07676-1$2DOI
100 1 $aFERNANDES, A. C.
245 $aGenome-wide detection of CNVs and their association with performance traits in broilers.$h[electronic resource]
260 $c2021
520 $aAbstract Background: Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results: We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions: Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens. Keywords: GWAS, Performance, CNVs, QTLs, qPCR
650 $aAnimal genetics
650 $aAnimal performance
650 $aGallus gallus
650 $aGenome-wide association study
650 $aQuantitative polymerase chain reaction
650 $aQuantitative trait loci
650 $aGallus Domesticus
650 $aGenética Animal
650 $aPerformance
653 $aCNVs
653 $aCopy number variations
653 $aDesempenho zootécnico
653 $aGWAS
653 $aQPCR
653 $aQTLs
700 1 $aSILVA, V. H. da
700 1 $aGOES, C. P.
700 1 $aMOREIRA, G. C. M.
700 1 $aGODOY, T. F.
700 1 $aIBELLI, A. M. G.
700 1 $aPEIXOTO, J. de O.
700 1 $aCANTAO, M. E.
700 1 $aLEDUR, M. C.
700 1 $aREZENDE, F. M. de
700 1 $aCOUTINHO, L. L.
773 $tBMC Genomics$gv. 22, n. 354, 2021.
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| 1. |  | FERNANDES, A. C.; SILVA, V. H. da; GOES, C. P.; MOREIRA, G. C. M.; GODOY, T. F.; IBELLI, A. M. G.; PEIXOTO, J. de O.; CANTAO, M. E.; LEDUR, M. C.; REZENDE, F. M. de; COUTINHO, L. L. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics, v. 22, n. 354, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
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