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Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

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...

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Autores principales: de Lima, Andressa O., Koltes, James E., Diniz, Wellison J. S., de Oliveira, Priscila S. N., Cesar, Aline S. M., Tizioto, Polyana C., Afonso, Juliana, de Souza, Marcela M., Petrini, Juliana, Rocha, Marina I. P., Cardoso, Tainã F., Neto, Adhemar Zerlotini, Coutinho, Luiz L., Mourão, Gerson B., Regitano, Luciana C. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064723/
https://www.ncbi.nlm.nih.gov/pubmed/32194642
http://dx.doi.org/10.3389/fgene.2020.00189
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author de Lima, Andressa O.
Koltes, James E.
Diniz, Wellison J. S.
de Oliveira, Priscila S. N.
Cesar, Aline S. M.
Tizioto, Polyana C.
Afonso, Juliana
de Souza, Marcela M.
Petrini, Juliana
Rocha, Marina I. P.
Cardoso, Tainã F.
Neto, Adhemar Zerlotini
Coutinho, Luiz L.
Mourão, Gerson B.
Regitano, Luciana C. A.
author_facet de Lima, Andressa O.
Koltes, James E.
Diniz, Wellison J. S.
de Oliveira, Priscila S. N.
Cesar, Aline S. M.
Tizioto, Polyana C.
Afonso, Juliana
de Souza, Marcela M.
Petrini, Juliana
Rocha, Marina I. P.
Cardoso, Tainã F.
Neto, Adhemar Zerlotini
Coutinho, Luiz L.
Mourão, Gerson B.
Regitano, Luciana C. A.
author_sort de Lima, Andressa O.
collection PubMed
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.
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spelling pubmed-70647232020-03-19 Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses de Lima, Andressa O. Koltes, James E. Diniz, Wellison J. S. de Oliveira, Priscila S. N. Cesar, Aline S. M. Tizioto, Polyana C. Afonso, Juliana de Souza, Marcela M. Petrini, Juliana Rocha, Marina I. P. Cardoso, Tainã F. Neto, Adhemar Zerlotini Coutinho, Luiz L. Mourão, Gerson B. Regitano, Luciana C. A. Front Genet Genetics 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. Frontiers Media S.A. 2020-03-04 /pmc/articles/PMC7064723/ /pubmed/32194642 http://dx.doi.org/10.3389/fgene.2020.00189 Text en Copyright © 2020 de Lima, Koltes, Diniz, de Oliveira, Cesar, Tizioto, Afonso, de Souza, Petrini, Rocha, Cardoso, Neto, Coutinho, Mourão and Regitano. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
de Lima, Andressa O.
Koltes, James E.
Diniz, Wellison J. S.
de Oliveira, Priscila S. N.
Cesar, Aline S. M.
Tizioto, Polyana C.
Afonso, Juliana
de Souza, Marcela M.
Petrini, Juliana
Rocha, Marina I. P.
Cardoso, Tainã F.
Neto, Adhemar Zerlotini
Coutinho, Luiz L.
Mourão, Gerson B.
Regitano, Luciana C. A.
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
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_short 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
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064723/
https://www.ncbi.nlm.nih.gov/pubmed/32194642
http://dx.doi.org/10.3389/fgene.2020.00189
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