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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
001 2145918
005 2022-11-17
008 2022 bl uuuu u00u1 u #d
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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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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Voltar
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Registro Completo
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Biblioteca(s): |
Embrapa Unidades Centrais. |
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Data corrente: |
23/06/1999 |
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Data da última atualização: |
30/03/2023 |
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Autoria: |
PICANCO, M.; LEITE, G. L. D.; MENDES, M. C.; BORGES, V. E. |
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Afiliação: |
MARCELO PICANÇO, Universidade Federal de Viçosa - UFV/Departamento de Biologia Animal; GERMANO LEÃO DEMOLIN LEITE, Universidade Federal de Viçosa - UFV/Departamento de Biologia Animal; MÁRCIO C. MENDES, EMPAER; VALDIVINO ENEDINO BORGES, EMPAER. |
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Título: |
Ataque de Atarsocoris brachiariae Becker, uma nova praga das pastagens em Mato Grosso, Brasil. |
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Ano de publicação: |
1999 |
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Fonte/Imprenta: |
Pesquisa Agropecuária Brasileira, Brasília, DF, v. 34, n. 5, p. 885-90, maio 1999 |
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Idioma: |
Português |
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Notas: |
Notas Científicas.
Título em inglês: Attack of Atarsocoris brachiariae Becker, a new pest of pasturelands in Mato Grosso, Brazil. |
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Conteúdo: |
Estudou-se o efeito da textura do solo, relevo, especie forrageira, idade e sistema de formacao da pastagem, sobre o ataque de Atarsocoris brachiariae. Nao foram observadas diferencas significativas entre as especies de forrageiras ou tipo de relevo quanto ao ataque da praga. As maiores densidades foram observadas em solos de textura arenosa, pastagens com mais de quatro anos, sistema de formacao convencional e na faixa de 20-30 cm de profundidade. O ataque foi em reboleiras, e a maior densidade ocorreu na regiao de transicao entre a area de pastagem morta e a area em que esta apresentava desenvolvimento normal. |
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Thesagro: |
Pastagem; Praga de Planta; Relevo; Textura do Solo. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/AI-SEDE/3034/1/PAB-201-96-NC-certa.pdf
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Marc: |
LEADER 01394naa a2200217 a 4500
001 1086277
005 2023-03-30
008 1999 bl uuuu u00u1 u #d
100 1 $aPICANCO, M.
245 $aAtaque de Atarsocoris brachiariae Becker, uma nova praga das pastagens em Mato Grosso, Brasil.$h[electronic resource]
260 $c1999
500 $aNotas Científicas. Título em inglês: Attack of Atarsocoris brachiariae Becker, a new pest of pasturelands in Mato Grosso, Brazil.
520 $aEstudou-se o efeito da textura do solo, relevo, especie forrageira, idade e sistema de formacao da pastagem, sobre o ataque de Atarsocoris brachiariae. Nao foram observadas diferencas significativas entre as especies de forrageiras ou tipo de relevo quanto ao ataque da praga. As maiores densidades foram observadas em solos de textura arenosa, pastagens com mais de quatro anos, sistema de formacao convencional e na faixa de 20-30 cm de profundidade. O ataque foi em reboleiras, e a maior densidade ocorreu na regiao de transicao entre a area de pastagem morta e a area em que esta apresentava desenvolvimento normal.
650 $aPastagem
650 $aPraga de Planta
650 $aRelevo
650 $aTextura do Solo
700 1 $aLEITE, G. L. D.
700 1 $aMENDES, M. C.
700 1 $aBORGES, V. E.
773 $tPesquisa Agropecuária Brasileira, Brasília, DF$gv. 34, n. 5, p. 885-90, maio 1999
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Embrapa Unidades Centrais (AI-SEDE) |
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| 1. |  | 0900875, RELATORIO TECNICO ANUAL. EMBRAPA. CNPSA, EMBRAPA-CNPSA, Concordia-SC
Biblioteca(s): Catálogo Coletivo de Periódicos Embrapa; Embrapa Acre; Embrapa Amapá; Embrapa Amazônia Oriental; Embrapa Pantanal. |   |
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