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Registro Completo |
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Biblioteca(s): |
Embrapa Pecuária Sudeste. |
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Data corrente: |
03/05/2021 |
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Data da última atualização: |
12/08/2021 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
BRUSCADIN, J. J.; SOUZA, M. M. DE; OLIVEIRA, K. S. DE; ROCHA, M. I. P.; AFONSO, J.; CARDOSO, T. F.; ZERLOTINI NETO, A.; COUTINHO, L. L.; NICIURA, S. C. M.; REGITANO, L. C. de A. |
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Afiliação: |
JENNIFER JESSICA BRUSCADIN, UFSCAR; MARCELA MARIA DE SOUZA, Iowa State University; KARINA SANTOS DE OLIVEIRA, UFSCAR; MARINA IBELLI PEREIRA ROCHA, UFSCAR; JULIANA AFONSO, USP ESALQ; TAINÃ FIGUEIREDO CARDOSO, FAPESP; ADHEMAR ZERLOTINI NETO, CNPTIA; LUIZ LEHMANN COUTINHO, USP ESALQ; SIMONE CRISTINA MEO NICIURA, CPPSE; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
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Título: |
Muscle allele-specifc expression QTLs may afect meat quality traits in Bos indicus. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Scientific Reports, v.11, p.1-14, 2021. |
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DOI: |
https://doi.org/10.1038/s41598-021-86782-2 |
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Idioma: |
Inglês |
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Notas: |
Article number: 7321. |
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Conteúdo: |
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specifc expression (ASE SNPs) were previously identifed in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specifc expression pattern may result from cis-regulatory SNPs, called allele-specifc expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfte sequencing (RRBS) obtained from 12 animals of the same population. We identifed 1134 aseQTLs associated with 126 diferent ASE SNPs. For 215 aseQTLs, one allele potentially afected the afnity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to afect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the frst report of aseQTLs identifcation in bovine muscle. Our fndings indicate that various cis-regulatory and epigenetic mechanisms can afect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. MenosSingle nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specifc expression (ASE SNPs) were previously identifed in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specifc expression pattern may result from cis-regulatory SNPs, called allele-specifc expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfte sequencing (RRBS) obtained from 12 animals of the same population. We identifed 1134 aseQTLs associated with 126 diferent ASE SNPs. For 215 aseQTLs, one allele potentially afected the afnity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to afect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the frst report of aseQTLs identifcation in bovine muscle. Our fndings indicate that various cis-regulatory and ... Mostrar Tudo |
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Palavras-Chave: |
Animal biotechnology; Functional genomics; Gene regulation. |
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Thesaurus Nal: |
Animal breeding; Gene expression; Genetic markers; Genetics; Genome; Genomics; Genotype. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/225126/1/Muscle-Allele-Specifc.pdf
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Marc: |
LEADER 02915naa a2200373 a 4500
001 2131644
005 2021-08-12
008 2021 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1038/s41598-021-86782-2$2DOI
100 1 $aBRUSCADIN, J. J.
245 $aMuscle allele-specifc expression QTLs may afect meat quality traits in Bos indicus.$h[electronic resource]
260 $c2021
500 $aArticle number: 7321.
520 $aSingle nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specifc expression (ASE SNPs) were previously identifed in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specifc expression pattern may result from cis-regulatory SNPs, called allele-specifc expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfte sequencing (RRBS) obtained from 12 animals of the same population. We identifed 1134 aseQTLs associated with 126 diferent ASE SNPs. For 215 aseQTLs, one allele potentially afected the afnity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to afect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the frst report of aseQTLs identifcation in bovine muscle. Our fndings indicate that various cis-regulatory and epigenetic mechanisms can afect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
650 $aAnimal breeding
650 $aGene expression
650 $aGenetic markers
650 $aGenetics
650 $aGenome
650 $aGenomics
650 $aGenotype
653 $aAnimal biotechnology
653 $aFunctional genomics
653 $aGene regulation
700 1 $aSOUZA, M. M. DE
700 1 $aOLIVEIRA, K. S. DE
700 1 $aROCHA, M. I. P.
700 1 $aAFONSO, J.
700 1 $aCARDOSO, T. F.
700 1 $aZERLOTINI NETO, A.
700 1 $aCOUTINHO, L. L.
700 1 $aNICIURA, S. C. M.
700 1 $aREGITANO, L. C. de A.
773 $tScientific Reports$gv.11, p.1-14, 2021.
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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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| Registros recuperados : 86 | |
| 15. |  | CHAGAS, S. S.; YAMAGISHI, M. E. B.; ZERLOTINI NETO, A.; SILVA, G. F. da; CANIATO, F. F. Cazymes, peptidases e lipases secretadas do fungo fitopatogênico Pseusopestalotiopsis gilvanii (CPAA222): uma abordagem genômica. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 6.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 16. | | CHAGAS, S. S.; YAMAGISHI, M. E. B.; ZERLOTINI NETO, A.; SILVA, G. F. da; CANIATO, F. F. Cazymes, peptidases e lipases secretadas do fungo fitopatogênico Pseusopestalotiopsis gilvanii (CPAA222): uma abordagem genômica. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 6.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 17. | | CONTEVILLE, L. C.; ANDRADE, B. G.; ZERLOTINI NETO, A.; MOURÃO, G.; COUTINHO, L. L.; REGITANO, L. C. de A. Carbohydrate active enzymes in metagenome-assembled genomes from ruminal and stool microbiomes of nelore cattle. In: BRAZILIAN CONGRESS OF GENETICS, 67., 2022, Natal. [Abstracts]. Ribeirão Preto: Sociedade Brasileira de Genética, 2022. p. 426. e-book. Na publicação: Adhemar Zerlotini, Luciana de Almeida Regitano.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| 18. | | SIMÕES, M.; BAHIA, D.; TORRES, K.; ZERLOTINI NETO, A.; ARTIGUENAVE, F.; FALCAO, P. R. K.; NESHICH, G.; OLIVEIRA, G. SNP identification in Schistosoma mansoni expressed genes. In: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional, 2005. p. 131. X-meeting 2005. Presented Posters. Na publicação: Paula Kuser.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 20. | | ZERLOTINI NETO, A.; NHANI JÚNIOR, A.; VIEIRA, F. D.; CINTRA, L. C.; MUDADU, M. de A.; FALCÃO, P. R. K.; GIACHETTO, P. F. Aplicações da bioinformática na agricultura. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; OLIVEIRA, S. R. de M.; MEIRA, C. A. A.; LUCHIARI JUNIOR, A.; BOLFE, E. L. (Ed.). Agricultura digital: pesquisa, desenvolvimento e inovação nas cadeias produtivas. Brasília, DF: Embrapa, 2020. cap. 10, p. 234-257.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 86 | |
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