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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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de Lima, Andressa O. [1] ; Koltes, James E. [2] ; Diniz, Wellison J. S. [1] ; de Oliveira, Priscila S. N. [3] ; Cesar, Aline S. M. [4] ; Tizioto, Polyana C. [5] ; Afonso, Juliana [1] ; de Souza, Marcela M. [2] ; Petrini, Juliana [6] ; Rocha, Marina I. P. [1] ; Cardoso, Taina F. [3] ; Neto, Adhemar Zerlotini [7] ; Coutinho, Luiz L. [8] ; Mourao, Gerson B. [8] ; Regitano, Luciana C. A. [3]
Total Authors: 15
Affiliation:
[1] Univ Fed Sao Carlos, Ctr Biol & Hlth Sci, Sao Carlos - Brazil
[2] Iowa State Univ, Dept Anim Sci, Ames, IA - USA
[3] Empresa Brazileira Pesquisa Agr, Embrapa Pecuaria Sudeste, Sao Carlos - Brazil
[4] Univ Sao Paulo, Dept Agroind Food & Nutr, Luiz de Queiroz Coll Agr, Piracicaba - Brazil
[5] NGS Genom Solut, Piracicaba - Brazil
[6] Univ Fed Alfenas, Exact Sci Inst, Alfenas - Brazil
[7] Empresa Brazileira Pesquisa Agr, Embrapa Informat Agr, Campinas - Brazil
[8] Univ Sao Paulo, Dept Anim Sci, Luiz de Queiroz Coll Agr, Piracicaba - Brazil
Total Affiliations: 8
Document type: Journal article
Source: FRONTIERS IN GENETICS; v. 11, MAR 4 2020.
Web of Science Citations: 0
Abstract

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. (AU)

FAPESP's process: 12/23638-8 - Molecular basis of meat quality in Nelore beef cattle
Grantee:Luciana Correia de Almeida Regitano
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 19/04089-2 - The Nelore hologenome: implications in beef quality and feed efficiency
Grantee:Luciana Correia de Almeida Regitano
Support Opportunities: Research Grants - eScience and Data Science Program - Thematic Grants