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Registro Completo |
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Biblioteca(s): |
Embrapa Pecuária Sudeste. |
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Data corrente: |
31/08/2022 |
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Data da última atualização: |
17/11/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
VIGNATO, B. S.; CESAR, A. S. M.; AFONSO, J.; MOREIRA, G. C. M.; POLETI, M. D.; PETRINI, J.; GARCIA, I. S.; CLEMENTE, L. G.; MOURÃO, G. B.; REGITANO, L. C. de A.; COUTINHO, L. L. |
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Afiliação: |
BÁRBARA SILVA VIGNATO, UNIVERSIDADE DE SÃO PAULO; ALINE SILVA MELLO CESAR, UNIVERSIDADE DE SÃO PAULO; JULIANA AFONSO, UNIVERSIDADE FEDERAL DE SÃO CARLOS; GABRIEL COSTA MONTEIRO MOREIRA, UNIVERSIDADE DE SÃO PAULO; MIRELE DAIANA POLETI, UNIVERSIDADE DE SÃO PAULO; JULIANA PETRINI, UNIVERSIDADE DE SÃO PAULO; INGRID SOARES GARCIA, UNIVERSIDADE DE SÃO PAULO; LUAN GASPAR CLEMENTE, UNIVERSIDADE DE SÃO PAULO; GERSON BARRETO MOURÃO, UNIVERSIDADE DE SÃO PAULO; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; LUIZ LEHMANN COUTINHO, UNIVERSIDADE DE SÃO PAULO. |
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Título: |
Integrative analysis between genome-wide association study and expression quantitative trait Loci reveals bovine muscle gene expression regulatory polymorphisms associated with intramuscular fat and backfat thickness. |
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Ano de publicação: |
2022 |
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Fonte/Imprenta: |
Frontiers in Genetics, v. 13, 935238, aug. 2022. |
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Páginas: |
15 p. |
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DOI: |
10.3389/fgene.2022.935238 |
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Idioma: |
Inglês |
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Conteúdo: |
Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle. MenosUnderstanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways... Mostrar Tudo |
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Palavras-Chave: |
Backfat thickness; Carcass and meat quality; Expression quantitative trait loci; Intramuscular fat content; Nellore cattle; RNA Seq; SNP. |
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Thesaurus Nal: |
Nellore. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1145918/1/IntegrativeAnalysisGenome.pdf
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Marc: |
LEADER 02780naa a2200361 a 4500
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024 7 $a10.3389/fgene.2022.935238$2DOI
100 1 $aVIGNATO, B. S.
245 $aIntegrative analysis between genome-wide association study and expression quantitative trait Loci reveals bovine muscle gene expression regulatory polymorphisms associated with intramuscular fat and backfat thickness.$h[electronic resource]
260 $c2022
300 $a15 p.
520 $aUnderstanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.
650 $aNellore
653 $aBackfat thickness
653 $aCarcass and meat quality
653 $aExpression quantitative trait loci
653 $aIntramuscular fat content
653 $aNellore cattle
653 $aRNA Seq
653 $aSNP
700 1 $aCESAR, A. S. M.
700 1 $aAFONSO, J.
700 1 $aMOREIRA, G. C. M.
700 1 $aPOLETI, M. D.
700 1 $aPETRINI, J.
700 1 $aGARCIA, I. S.
700 1 $aCLEMENTE, L. G.
700 1 $aMOURÃO, G. B.
700 1 $aREGITANO, L. C. de A.
700 1 $aCOUTINHO, L. L.
773 $tFrontiers in Genetics$gv. 13, 935238, aug. 2022.
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Embrapa Pecuária Sudeste (CPPSE) |
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| 1. |  | VIGNATO, B. S.; CESAR, A. S. M.; AFONSO, J.; MOREIRA, G. C. M.; POLETI, M. D.; PETRINI, J.; GARCIA, I. S.; CLEMENTE, L. G.; MOURÃO, G. B.; REGITANO, L. C. de A.; COUTINHO, L. L. Integrative analysis between genome-wide association study and expression quantitative trait Loci reveals bovine muscle gene expression regulatory polymorphisms associated with intramuscular fat and backfat thickness. Frontiers in Genetics, v. 13, 935238, aug. 2022. 15 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| Registros recuperados : 1 | |
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