AustralieFrV1, Ncbi, Curation, bibRecord, 001998

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

Identifieur interne : 001998 ( Ncbi/Curation ); précédent : 001997; suivant : 001999

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

Auteurs : Y. Ramayo-Caldas [France] ; M R S. Fortes [Australie] ; N J Hudson [Australie] ; L R Porto-Neto [Australie] ; S. Bolormaa [Australie] ; W. Barendse [Australie] ; M. Kelly [Australie] ; S S Moore [Australie] ; M E Goddard [Australie] ; S A Lehnert [Australie] ; A. Reverter [Australie]

Source :

Journal of animal science [ 1525-3163 ] ; 2014.

RBID : pubmed:24778332

Descripteurs français

English descriptors

KwdEn :
- Adiposity (genetics), Adiposity (physiology), Animals, Cattle (anatomy & histology), Cattle (genetics), Cattle (physiology), Forkhead Transcription Factors (genetics), Forkhead Transcription Factors (physiology), Gene Expression Regulation (genetics), Gene Expression Regulation (physiology), Gene Regulatory Networks (genetics), Genetic Markers (genetics), Genome-Wide Association Study (veterinary), Hepatocyte Nuclear Factor 4 (genetics), Hepatocyte Nuclear Factor 4 (physiology), Meat (standards), Muscle, Skeletal (physiology), Quantitative Trait, Heritable, Transcription Factors (genetics), Transcription Factors (physiology).
MESH :
- chemical , genetics : Forkhead Transcription Factors, Genetic Markers, Hepatocyte Nuclear Factor 4, Transcription Factors.
- anatomy & histology : Cattle.
- genetics : Adiposity, Cattle, Gene Expression Regulation, Gene Regulatory Networks.
- physiology : Adiposity, Cattle, Forkhead Transcription Factors, Gene Expression Regulation, Hepatocyte Nuclear Factor 4, Muscle, Skeletal, Transcription Factors.
- standards : Meat.
- veterinary : Genome-Wide Association Study.
- Animals, Quantitative Trait, Heritable.

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.

DOI: 10.2527/jas.2013-7484
PubMed: 24778332

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pubmed:24778332

Le document en format XML

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<author><name sortKey="Reverter, A" sort="Reverter, A" uniqKey="Reverter A" first="A" last="Reverter">A. Reverter</name>
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<term>Adiposity (physiology)</term>
<term>Animals</term>
<term>Cattle (anatomy & histology)</term>
<term>Cattle (genetics)</term>
<term>Cattle (physiology)</term>
<term>Forkhead Transcription Factors (genetics)</term>
<term>Forkhead Transcription Factors (physiology)</term>
<term>Gene Expression Regulation (genetics)</term>
<term>Gene Expression Regulation (physiology)</term>
<term>Gene Regulatory Networks (genetics)</term>
<term>Genetic Markers (genetics)</term>
<term>Genome-Wide Association Study (veterinary)</term>
<term>Hepatocyte Nuclear Factor 4 (genetics)</term>
<term>Hepatocyte Nuclear Factor 4 (physiology)</term>
<term>Meat (standards)</term>
<term>Muscle, Skeletal (physiology)</term>
<term>Quantitative Trait, Heritable</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (physiology)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Adiposité (génétique)</term>
<term>Adiposité (physiologie)</term>
<term>Animaux</term>
<term>Bovins (anatomie et histologie)</term>
<term>Bovins (génétique)</term>
<term>Bovins (physiologie)</term>
<term>Caractère quantitatif héréditaire</term>
<term>Facteur nucléaire hépatocytaire HNF-4 (génétique)</term>
<term>Facteur nucléaire hépatocytaire HNF-4 (physiologie)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (physiologie)</term>
<term>Facteurs de transcription Forkhead (génétique)</term>
<term>Facteurs de transcription Forkhead (physiologie)</term>
<term>Marqueurs génétiques (génétique)</term>
<term>Muscles squelettiques (physiologie)</term>
<term>Régulation de l'expression des gènes (génétique)</term>
<term>Régulation de l'expression des gènes (physiologie)</term>
<term>Réseaux de régulation génique (génétique)</term>
<term>Viande (normes)</term>
<term>Étude d'association pangénomique (médecine vétérinaire)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Forkhead Transcription Factors</term>
<term>Genetic Markers</term>
<term>Hepatocyte Nuclear Factor 4</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Bovins</term>
</keywords>
<keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Cattle</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adiposity</term>
<term>Cattle</term>
<term>Gene Expression Regulation</term>
<term>Gene Regulatory Networks</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Adiposité</term>
<term>Bovins</term>
<term>Facteur nucléaire hépatocytaire HNF-4</term>
<term>Facteurs de transcription</term>
<term>Facteurs de transcription Forkhead</term>
<term>Marqueurs génétiques</term>
<term>Régulation de l'expression des gènes</term>
<term>Réseaux de régulation génique</term>
</keywords>
<keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Étude d'association pangénomique</term>
</keywords>
<keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Viande</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Adiposité</term>
<term>Bovins</term>
<term>Facteur nucléaire hépatocytaire HNF-4</term>
<term>Facteurs de transcription</term>
<term>Facteurs de transcription Forkhead</term>
<term>Muscles squelettiques</term>
<term>Régulation de l'expression des gènes</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Adiposity</term>
<term>Cattle</term>
<term>Forkhead Transcription Factors</term>
<term>Gene Expression Regulation</term>
<term>Hepatocyte Nuclear Factor 4</term>
<term>Muscle, Skeletal</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Meat</term>
</keywords>
<keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Genome-Wide Association Study</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Quantitative Trait, Heritable</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Caractère quantitatif héréditaire</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
</record>

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

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

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