Gene co-expression network analysis for porcine intramuscular fatty acid composition
C. Sebastià,
M. Gallopin,
Y. Ramayo-Caldas,
J. Estellé,
J. Valdés-Hernández,
A. Castelló,
A. Sánchez,
D. Crespo-Piazuelo,
J.M. Folch
Affiliations
C. Sebastià
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain; Corresponding author.
M. Gallopin
Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1, Avenue de la Terrasse, Bâtiment 21, 91190 Gif-sur-Yvette, France
Y. Ramayo-Caldas
Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
J. Estellé
Université Paris-Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy-en-Josas, France
J. Valdés-Hernández
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
A. Castelló
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
A. Sánchez
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
D. Crespo-Piazuelo
Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain; R&D Department, Cuarte S.L., Grupo Jorge, Autov. Zaragoza-Logroño, km.9, 50120 Monzalbarba, Spain
J.M. Folch
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain
In pigs, meat quality depends markedly on the fatty acid (FA) content and composition of the intramuscular fat, which is partly determined by the gene expression in this tissue. The aim of this work was to identify the link between muscle gene expression and its FA composition. In an (Iberian × Duroc) × Duroc backcrossed pig population, we identified modules of co-expressed genes, and correlation analyses were performed for each of them versus the phenotypes, finding four relevant modules. Two of the modules were positively correlated with saturated FAs (SFAs) and monounsaturated FAs (MUFAs), while negatively correlated with polyunsaturated FAs (PUFAs) and the omega-6/omega-3 ratio. The gene-enrichment analysis showed that these modules had over-representation of pathways related with the biosynthesis of unsaturated FAs, the Peroxisome proliferator-activated receptor signalling pathway and FA elongation. The two other relevant modules were positively correlated with PUFA and the n-6/n-3 ratio, but negatively correlated with SFA and MUFA. In this case, they had an over-representation of pathways related with fatty and amino acid degradation, and with oxidative phosphorylation. Using a graphical Gaussian model, we inferred a network of connections between the genes within each module. The first module had 52 genes with 87 connections, and the most connected genes were ADIPOQ, which is related with FA oxidation, and ELOVL6 and FABP4, both involved in FA metabolism. The second module showed 196 genes connected by 263 edges, being FN1 and MAP3K11 the most connected genes. On the other hand, the third module had 161 genes connected by 251 edges and ATG13 was the top neighbouring gene, while the fourth module had 224 genes and 655 connections, and its most connected genes were related with mitochondrial pathways. Overall, this work successfully identified relevant muscle gene networks and modules linked with FA composition, providing further insights on how the physiology of the pigs influences FA composition.
