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Front Genet. 2019 Mar 13;10:210. doi: 10.3389/fgene.2019.00210. eCollection 2019.

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle.

Author information

1
Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
2
Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.
3
Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil.
4
Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
5
Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil.
6
Graduate School of Public Health and Health Policy, The City University of New York, New York, NY, United States.
7
Department of Aquaculture, Technical University of Denmark, Kongens Lyngby, Denmark.

Abstract

Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.

KEYWORDS:

AMPK pathway; RNA sequencing; co-expression analysis; intramuscular fat; tenderness

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