Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses.
Autor(a) principal: | |
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Data de Publicação: | 2020 |
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/1124356 https://doi.org/10.3389/fgene.2020.00189 |
Resumo: | Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle. |
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Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses.Longissimus thoracisBiomarcadoresExpressão gênicaFeed efficiencyHub genesSystems biologyWGCNABos IndicusGene expressionFeed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.Article 189. Na publicação: Luciana C. A. Regitano.ANDRESSA O. DE LIMA, UFSCar; JAMES E. KOLTES, Iowa State University; WELLISON J. S. DINIZ, UFSCar; PRISCILA S. N. DE OLIVEIRA; ALINE S. M. CESAR, Esalq/USP; POLYANA C. TIZIOTO, NGS Genomic Solution; JULIANA AFONSO, UFSCar; MARCELA M. DE SOUZA, Iowa State University; JULIANA PETRINI, UNIFAL; MARINA I. P. ROCHA, UFSCar; TAINÃ F. CARDOSO; ADHEMAR ZERLOTINI NETO, CNPTIA; LUIZ L. COUTINHO, Esalq/USP; GERSON B. MOURÃO, Esalq/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE.LIMA, A. O. deKOLTES, J. E.DINIZ, W. J. S.OLIVEIRA, P. S. N. deCESAR, A. S. M.TIZIOTO, P. L.AFONSO, J.SOUZA, M. de S.PETRINI, J.ROCHA, M. I. P.CARDOSO, T. F.ZERLOTINI NETO, A.COUTINHO, L. L.MOURÃO, G. B.REGITANO, L. C. de A.2020-08-15T04:11:44Z2020-08-15T04:11:44Z2020-08-142020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFrontiers in Genetics, v. 11, p. 1-14, Mar. 2020.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124356https://doi.org/10.3389/fgene.2020.00189enginfo: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:EMBRAPA2020-08-15T04:11:52Zoai:www.alice.cnptia.embrapa.br:doc/1124356Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542020-08-15T04:11:52falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542020-08-15T04:11:52Repositório 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 |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
title |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
spellingShingle |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. LIMA, A. O. de Longissimus thoracis Biomarcadores Expressão gênica Feed efficiency Hub genes Systems biology WGCNA Bos Indicus Gene expression |
title_short |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
title_full |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
title_fullStr |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
title_full_unstemmed |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
title_sort |
Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses. |
author |
LIMA, A. O. de |
author_facet |
LIMA, A. O. de KOLTES, J. E. DINIZ, W. J. S. OLIVEIRA, P. S. N. de CESAR, A. S. M. TIZIOTO, P. L. AFONSO, J. SOUZA, M. de S. PETRINI, J. ROCHA, M. I. P. CARDOSO, T. F. ZERLOTINI NETO, A. COUTINHO, L. L. MOURÃO, G. B. REGITANO, L. C. de A. |
author_role |
author |
author2 |
KOLTES, J. E. DINIZ, W. J. S. OLIVEIRA, P. S. N. de CESAR, A. S. M. TIZIOTO, P. L. AFONSO, J. SOUZA, M. de S. PETRINI, J. ROCHA, M. I. P. CARDOSO, T. F. ZERLOTINI NETO, A. COUTINHO, L. L. MOURÃO, G. B. REGITANO, L. C. de A. |
author2_role |
author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
ANDRESSA O. DE LIMA, UFSCar; JAMES E. KOLTES, Iowa State University; WELLISON J. S. DINIZ, UFSCar; PRISCILA S. N. DE OLIVEIRA; ALINE S. M. CESAR, Esalq/USP; POLYANA C. TIZIOTO, NGS Genomic Solution; JULIANA AFONSO, UFSCar; MARCELA M. DE SOUZA, Iowa State University; JULIANA PETRINI, UNIFAL; MARINA I. P. ROCHA, UFSCar; TAINÃ F. CARDOSO; ADHEMAR ZERLOTINI NETO, CNPTIA; LUIZ L. COUTINHO, Esalq/USP; GERSON B. MOURÃO, Esalq/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
dc.contributor.author.fl_str_mv |
LIMA, A. O. de KOLTES, J. E. DINIZ, W. J. S. OLIVEIRA, P. S. N. de CESAR, A. S. M. TIZIOTO, P. L. AFONSO, J. SOUZA, M. de S. PETRINI, J. ROCHA, M. I. P. CARDOSO, T. F. ZERLOTINI NETO, A. COUTINHO, L. L. MOURÃO, G. B. REGITANO, L. C. de A. |
dc.subject.por.fl_str_mv |
Longissimus thoracis Biomarcadores Expressão gênica Feed efficiency Hub genes Systems biology WGCNA Bos Indicus Gene expression |
topic |
Longissimus thoracis Biomarcadores Expressão gênica Feed efficiency Hub genes Systems biology WGCNA Bos Indicus Gene expression |
description |
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-08-15T04:11:44Z 2020-08-15T04:11:44Z 2020-08-14 2020 |
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. 11, p. 1-14, Mar. 2020. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124356 https://doi.org/10.3389/fgene.2020.00189 |
identifier_str_mv |
Frontiers in Genetics, v. 11, p. 1-14, Mar. 2020. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124356 https://doi.org/10.3389/fgene.2020.00189 |
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) |
instacron_str |
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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1794503494815711232 |