A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle

Ramayo-Caldas, Y., Fortes, M. R. S., Hudson, N. J., Porto-Neto, L. R., Bolormaa, S., Barendse, W., Kelly, M., Moore, S. S., Goddard, M. E., Lehnert, S. A. and Reverter, A. (2014) A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle. Journal of Animal Science, 92 7: 2832-2845. doi:10.2527/jas.2013-7484


Author Ramayo-Caldas, Y.
Fortes, M. R. S.
Hudson, N. J.
Porto-Neto, L. R.
Bolormaa, S.
Barendse, W.
Kelly, M.
Moore, S. S.
Goddard, M. E.
Lehnert, S. A.
Reverter, A.
Title A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle
Formatted title
A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle
Journal name Journal of Animal Science   Check publisher's open access policy
ISSN 0021-8812
1525-3163
Publication date 2014-07
Sub-type Article (original research)
DOI 10.2527/jas.2013-7484
Open Access Status
Volume 92
Issue 7
Start page 2832
End page 2845
Total pages 14
Place of publication Champaign, IL, United States
Publisher American Society of Animal Science
Collection year 2015
Language eng
Formatted abstract
High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARGC1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.
Keyword Association weight matrix
Beef quality
Fat deposition
Genomewide association study
Marbling
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2015 Collection
 
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
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