Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

Wellison J. S. Diniz; Gianluca Mazzoni; Luiz L. Coutinho; Priyanka Banerjee; Ludwig Geistlinger; Aline S. M. Cesar; Francesca Bertolini; Juliana Afonso; Priscila S. N. de Oliveira; Polyana C. Tizioto; Haja Kadarmideen; Luciana C. A. Regitano

doi:10.3389/fgene.2019.00210

Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

Wellison J. S. Diniz, Gianluca Mazzoni, Luiz L. Coutinho, Priyanka Banerjee, Ludwig Geistlinger, Aline S. M. Cesar, Francesca Bertolini, Juliana Afonso, Priscila S. N. de Oliveira, Polyana C. Tizioto, Haja Kadarmideen, Luciana C. A. Regitano^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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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.

Original language	English
Article number	210
Journal	Frontiers in Genetics
Volume	10
Number of pages	12
ISSN	1664-8021
DOIs	https://doi.org/10.3389/fgene.2019.00210
Publication status	Published - 2019
Externally published	Yes

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Diniz, W. J. S., Mazzoni, G., Coutinho, L. L., Banerjee, P., Geistlinger, L., Cesar, A. S. M., Bertolini, F., Afonso, J., de Oliveira, P. S. N., Tizioto, P. C., Kadarmideen, H., & Regitano, L. C. A. (2019). Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle. Frontiers in Genetics, 10, Article 210. https://doi.org/10.3389/fgene.2019.00210

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title = "Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle",

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.",

author = "Diniz, {Wellison J. S.} and Gianluca Mazzoni and Coutinho, {Luiz L.} and Priyanka Banerjee and Ludwig Geistlinger and Cesar, {Aline S. M.} and Francesca Bertolini and Juliana Afonso and {de Oliveira}, {Priscila S. N.} and Tizioto, {Polyana C.} and Haja Kadarmideen and Regitano, {Luciana C. A.}",

year = "2019",

doi = "10.3389/fgene.2019.00210",

language = "English",

volume = "10",

journal = "Frontiers in Genetics",

issn = "1664-8021",

publisher = "Frontiers Media S.A",

}

Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle. / Diniz, Wellison J. S.; Mazzoni, Gianluca; Coutinho, Luiz L. et al.
In: Frontiers in Genetics, Vol. 10, 210, 2019.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

AU - Diniz, Wellison J. S.

AU - Mazzoni, Gianluca

AU - Coutinho, Luiz L.

AU - Banerjee, Priyanka

AU - Geistlinger, Ludwig

AU - Cesar, Aline S. M.

AU - Bertolini, Francesca

AU - Afonso, Juliana

AU - de Oliveira, Priscila S. N.

AU - Tizioto, Polyana C.

AU - Kadarmideen, Haja

AU - Regitano, Luciana C. A.

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

U2 - 10.3389/fgene.2019.00210

DO - 10.3389/fgene.2019.00210

M3 - Journal article

C2 - 30930938

SN - 1664-8021

VL - 10

JO - Frontiers in Genetics

JF - Frontiers in Genetics

M1 - 210

ER -

Detection of co-expressed pathway modules associated with mineral concentration and meat quality in Nelore cattle

Abstract

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