Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle.
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1106256 |
Resumo: | Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer?s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle. |
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Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle.Qualidade da carneMaciez da carneCarneGado de CorteBeefBeef cattleBeef qualityBeef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer?s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.Tássia Mangetti Gonçalves, USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; James E. Koltes, Iowa State University; Aline Silva Mello Cesar, USP; Sónia Cristina da Silva Andrade, USP; Gerson Barreto Mourão, USP; Gustavo Gasparin, USP; Gabriel Costa Monteiro Moreira, USP; Elyn Fritz-Waters, Iowa State University; James M. Reecy, Iowa State University; Luiz Lehmann Coutinho, USP.GONÇALVES, T. M.REGITANO, L. C. de A.KOLTES, J. E.CESAR, A. S. M.ANDRADE, S. C. da S.MOURAO, G. B.GASPARIN, G.MOREIRA, G. C. M.FRITZ-WATERS, E.REECY, J. M.COUTINHO, L. L.2019-02-20T00:35:57Z2019-02-20T00:35:57Z2019-02-1920182019-02-20T00:35:57Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFrontiers in Genetics, v.9, n. 441, p. 1-18, 2018.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1106256enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2019-02-20T00:36:04Zoai:www.alice.cnptia.embrapa.br:doc/1106256Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542019-02-20T00:36:04falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542019-02-20T00:36:04Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
title |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
spellingShingle |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. GONÇALVES, T. M. Qualidade da carne Maciez da carne Carne Gado de Corte Beef Beef cattle Beef quality |
title_short |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
title_full |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
title_fullStr |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
title_full_unstemmed |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
title_sort |
Gene co-expression analysis indicates potential pathways and regulators of beef tenderness in Nellore cattle. |
author |
GONÇALVES, T. M. |
author_facet |
GONÇALVES, T. M. REGITANO, L. C. de A. KOLTES, J. E. CESAR, A. S. M. ANDRADE, S. C. da S. MOURAO, G. B. GASPARIN, G. MOREIRA, G. C. M. FRITZ-WATERS, E. REECY, J. M. COUTINHO, L. L. |
author_role |
author |
author2 |
REGITANO, L. C. de A. KOLTES, J. E. CESAR, A. S. M. ANDRADE, S. C. da S. MOURAO, G. B. GASPARIN, G. MOREIRA, G. C. M. FRITZ-WATERS, E. REECY, J. M. COUTINHO, L. L. |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Tássia Mangetti Gonçalves, USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; James E. Koltes, Iowa State University; Aline Silva Mello Cesar, USP; Sónia Cristina da Silva Andrade, USP; Gerson Barreto Mourão, USP; Gustavo Gasparin, USP; Gabriel Costa Monteiro Moreira, USP; Elyn Fritz-Waters, Iowa State University; James M. Reecy, Iowa State University; Luiz Lehmann Coutinho, USP. |
dc.contributor.author.fl_str_mv |
GONÇALVES, T. M. REGITANO, L. C. de A. KOLTES, J. E. CESAR, A. S. M. ANDRADE, S. C. da S. MOURAO, G. B. GASPARIN, G. MOREIRA, G. C. M. FRITZ-WATERS, E. REECY, J. M. COUTINHO, L. L. |
dc.subject.por.fl_str_mv |
Qualidade da carne Maciez da carne Carne Gado de Corte Beef Beef cattle Beef quality |
topic |
Qualidade da carne Maciez da carne Carne Gado de Corte Beef Beef cattle Beef quality |
description |
Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer?s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018 2019-02-20T00:35:57Z 2019-02-20T00:35:57Z 2019-02-19 2019-02-20T00:35:57Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Frontiers in Genetics, v.9, n. 441, p. 1-18, 2018. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1106256 |
identifier_str_mv |
Frontiers in Genetics, v.9, n. 441, p. 1-18, 2018. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1106256 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
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Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
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EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503471581364224 |