Title:	Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses.
Authors:	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.
Affiliation:	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.
Date Issued:	2020
Citation:	Frontiers in Genetics, v. 11, p. 1-14, Mar. 2020.
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.
Thesagro:	Bos Indicus
NAL Thesaurus:	Gene expression
Keywords:	Longissimus thoracis Biomarcadores Expressão gênica Feed efficiency Hub genes Systems biology WGCNA
DOI:	https://doi.org/10.3389/fgene.2020.00189
Notes:	Article 189. Na publicação: Luciana C. A. Regitano.
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CNPTIA)