Puig-Oliveras A, Ballester M, Corominas J, Revilla M, Estellé J, Fernández AI, Ramayo-Caldas Y, Folch JM. A co-association network analysis of the genetic determination of pig conformation, growth and fatness. PLoS One. 2014;9:e114862.
Ayuso M, Fernández A, Núñez Y, Benítez R, Isabel B, Barragán C, Fernández AI, Rey AI, Medrano JF, Cánovas Á, et al. Comparative analysis of muscle transcriptome between pig genotypes identifies genes and regulatory mechanisms associated to growth, fatness and metabolism. PLoS One. 2015;10:e145162.
Wu T, Zhang Z, Yuan Z, Lo LJ, Chen J, Wang Y, Peng J. Distinctive genes determine different intramuscular fat and muscle fiber ratios of the longissimus dorsi muscles in Jinhua and landrace pigs. PLoS One. 2013;8:e53181.
Hocquette JF, Gondret F, Baéza E, Médale F, Jurie C, Pethick DW. Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, and identification of putative markers. Animal. 2010;4:303–19.
Gerbens F, Jansen A, van Erp AJ, Harders F, Meuwissen TH, Rettenberger G, Veerkamp JH, Te PM. The adipocyte fatty acid-binding protein locus: characterization and association with intramuscular fat content in pigs. Mamm Genome. 1998;9:1022–6.
Essen-Gustavsson B, Karlsson A, Lundstrom K, Enfalt AC. Intramuscular fat and muscle fibre lipid contents in halothane-gene-free pigs fed high or low protein diets and its relation to meat quality. Meat Sci. 1994;38:269–77.
Guo B, Kongsuwan K, Greenwood PL, Zhou G, Zhang W, Dalrymple BP. A gene expression estimator of intramuscular fat percentage for use in both cattle and sheep. J Anim Sci Biotechnol. 2014;5:35.
Ovilo C, Benitez R, Fernandez A, Nunez Y, Ayuso M, Fernandez AI, Rodriguez C, Isabel B, Rey AI, Lopez-Bote C, et al. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genomics. 2014;15:413.
Wood JD, Enser M, Fisher AV, Nute GR, Sheard PR, Richardson RI, Hughes SI, Whittington FM. Fat deposition, fatty acid composition and meat quality: a review. Meat Sci. 2008;78:343–58.
Cameron ND, Enser M, Nute GR, Whittington FM, Penman JC, Fisken AC, Perry AM, Wood JD. Genotype with nutrition interaction on fatty acid composition of intramuscular fat and the relationship with flavour of pig meat. Meat Sci. 2000;55:187–95.
Blanchard PJ, Willis MB, Warkup CC, Ellis M. The influence of carcass backfat and intramuscular fat level on pork eating quality. J Sci Food Agr. 2000;80:145–51.
Fan B, ZQ D, Rothschild MF. The fat mass and obesity-associated (FTO) gene is associated with intramuscular fat content and growth rate in the pig. Anim Biotechnol. 2009;20:58–70.
Cho KH, Kim MJ, Jeon GJ, Chung HY. Association of genetic variants for FABP3 gene with back fat thickness and intramuscular fat content in pig. Mol Biol Rep. 2011;38:2161–6.
Yang H, Huang X, Zeng Z, Zhang W, Liu C, Fang S, Huang L, Chen C. Genome-wide association analysis for blood lipid traits measured in three pig populations reveals a substantial level of genetic heterogeneity. PLoS One. 2015;10:e131667.
Chen Q, Zeng Y, Wang H, Yang L, Yang Y, Zhu H, Shi Y, Chen W, Hu Y. Molecular characterization and expression analysis of NDUFS4 gene in m. Longissimus dorsi of Laiwu pig (Sus Scrofa). Mol Biol Rep. 2013;40:1599–608.
Cui JX, Chen W, Zeng YQ. Development of FQ-PCR method to determine the level of ADD1 expression in fatty and lean pigs. Genet Mol Res. 2015;14:13924–31.
Cui J, Chen W, Liu J, Xu T, Zeng Y. Study on quantitative expression of PPARgamma and ADRP in muscle and its association with intramuscular fat deposition of pig. Spring. 2016;5:1501.
Zhang S, Shen L, Xia Y, Yang Q, Li X, Tang G, Jiang Y, Wang J, Li M, Zhu L. DNA methylation landscape of fat deposits and fatty acid composition in obese and lean pigs. Sci Rep-UK. 2016;6:35063.
Li M, Wu H, Luo Z, Xia Y, Guan J, Wang T, Gu Y, Chen L, Zhang K, Ma J, et al. An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun. 2012;3:850.
Zhao Y, Li J, Liu H, Xi Y, Xue M, Liu W, Zhuang Z, Lei M. Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. BMC Genomics. 2015;16:377.
Choi M, Lee J, Le MT, Nguyen DT, Park S, Soundrarajan N, Schachtschneider KM, Kim J, Park J, Kim J, et al. Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA Res. 2015;22:343–55.
Ramayo-Caldas Y, Mach N, Esteve-Codina A, Corominas J, Castello A, Ballester M, Estelle J, Ibanez-Escriche N, Fernandez AI, Perez-Enciso M, et al. Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition. BMC Genomics. 2012;13:547.
Huang Y, Sun J, Zhang L, Li C, Womack JE, Li Z, Lan X, Lei C, Zhang C, Zhao X, et al. Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep-UK. 2014;4:6546.
Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006;7:191.
Kramer A, Green J, Pollard JJ, Tugendreich S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014;30:523–30.
Ayuso M, Fernandez A, Nunez Y, Benitez R, Isabel B, Fernandez AI, Rey AI, Gonzalez-Bulnes A, Medrano JF, Canovas A, et al. Developmental stage, muscle and genetic type modify muscle transcriptome in pigs: effects on gene expression and regulatory factors involved in growth and metabolism. PLoS One. 2016;11:e167858.
Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W. MOABS: model based analysis of bisulfite sequencing data. Genome Biol. 2014;15:R38.
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
Munoz G, Ovilo C, Noguera JL, Sanchez A, Rodriguez C, Silio L. Assignment of the fatty acid synthase (FASN) gene to pig chromosome 12 by physical and linkage mapping. Anim Genet. 2003;34:234–5.
Sevane N, Armstrong E, Cortés O, Wiener P, Wong RP, Dunner S. Association of bovine meat quality traits with genes included in the PPARG and PPARGC1A networks. Meat Sci. 2013;94:328–35.
Davoli R, Braglia S, Zappaterra M, Redeghieri C, Comella M, Zambonelli P. Association and expression analysis of porcine ACLY gene related to growth and carcass quality traits in Italian large white and Italian Duroc breeds. Livest Sci. 2014;165:1–7.
Lee H, Park WJ. Unsaturated fatty acids, desaturases, and human health. J Med Food. 2014;17:189–97.
Xing K, Zhu F, Zhai L, Chen S, Tan Z, Sun Y, Hou Z, Wang C. Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data. Sci Rep-UK. 2016;6:23219.
Zulkifli RM, Parr T, Salter AM, Brameld JM. Regulation of ovine and porcine stearoyl coenzyme a desaturase gene promoters by fatty acids and sterols. J Anim Sci. 2010;88:2565–75.
Bessa RJB, Hughes RA, Jeronimo E, Moreira OC, Prates JAM, Doran O. Effect of pig breed and dietary protein level on selected fatty acids and stearoyl-coenzyme a desaturase protein expression in longissimus muscle and subcutaneous fat. J Anim Sci. 2013;91:4540–6.
Malerba G, Schaeffer L, Xumerle L, Klopp N, Trabetti E, Biscuola M, Cavallari U, Galavotti R, Martinelli N, Guarini P, et al. SNPs of the FADS gene cluster are associated with polyunsaturated fatty acids in a cohort of patients with cardiovascular disease. Lipids. 2008;43:289–99.
Ačimovič J, Rozman D. Steroidal triterpenes of cholesterol synthesis. Molecules. 2013;18:4002–17.
Mazein A, Watterson S, Hsieh W, Griffiths WJ, Ghazal P. A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway. Biochem Pharmacol. 2013;86:56–66.
Xing K, Zhu F, Zhai L, Liu H, Wang Y, Wang Z, Chen S, Hou Z, Wang C. Integration of transcriptome and whole genomic resequencing data to identify key genes affecting swine fat deposition. PLoS One. 2015;10:e122396.
Stupka N, Kintakas C, White JD, Fraser FW, Hanciu M, Aramaki-Hattori N, Martin S, Coles C, Collier F, Ward AC, et al. Versican processing by a disintegrin-like and metalloproteinase domain with thrombospondin-1 repeats proteinases-5 and -15 facilitates myoblast fusion. J Biol Chem. 2013;288(3):1907–17.
Cao Y. Angiogenesis and vascular functions in modulation of obesity, adipose metabolism, and insulin sensitivity. Cell Metab. 2013;18:478–89.
Lim KS, Lee KT, Park JE, Chung WH, Jang GW, Choi BH, Hong KC, Kim TH. Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing. Anim Genet. 2016; doi:10.1111/age.12518.
Zappaterra M, Deserti M, Mazza R, Braglia S, Zambonelli P, Davoli R. A gene and protein expression study on four porcine genes related to intramuscular fat deposition. Meat Sci. 2016;121:27–32.
Canovas A, Estany J, Tor M, Pena RN, Doran O. Acetyl-CoA carboxylase and stearoyl-CoA desaturase protein expression in subcutaneous adipose tissue is reduced in pigs selected for decreased backfat thickness at constant intramuscular fat content. J Anim Sci. 2009;87:3905–14.
Gallardo D, Quintanilla R, Varona L, Diaz I, Ramirez O, Pena RN, Amills M. Polymorphism of the pig acetyl-coenzyme a carboxylase alpha gene is associated with fatty acid composition in a Duroc commercial line. Anim Genet. 2009;40:410–7.
Henriquez-Rodriguez E, Tor M, Pena RN, Estany J. A polymorphism in the stearoyl-CoA desaturase gene promoter increases monounsaturated fatty acid content in dry-cured ham. Meat Sci. 2015;106:38–43.
Serão NVL, Veroneze R, Ribeiro AMF, Verardo LL, Braccini Neto J, Gasparino E, Campos CF, Lopes PS, Guimarães SEF. Candidate gene expression and intramuscular fat content in pigs. J Anim Breed Genet. 2011;128:28–34.
Shen Q, Bai Y, Chang KC, Wang Y, Burris TP, Freedman LP, Thompson CC, Nagpal S. Liver X receptor-retinoid X receptor (LXR-RXR) heterodimer cistrome reveals coordination of LXR and AP1 signaling in keratinocytes. J Biol Chem. 2011;286:14554–63.
Boyle KB, Hadaschik D, Virtue S, Cawthorn WP, Ridley SH, O'Rahilly S, Siddle K. The transcription factors Egr1 and Egr2 have opposing influences on adipocyte differentiation. Cell Death Differ. 2009;16:782–9.
Yang HW, Xia T, Chen ZL, Feng SQ, Peng Y, Zhou L, Gan L, Yang ZQ. Cloning, chromosomal localization and expression patterns of porcine Kruppel-like factors 4, −5, −7 and the early growth response factor 2. Biotechnol Lett. 2006;29:157–63.
Heckmann BL, Zhang X, Xie X, Saarinen A, Lu X, Yang X, Liu J. Defective adipose lipolysis and altered global energy metabolism in mice with adipose overexpression of the lipolytic inhibitor G0/G1 switch gene 2 (G0S2). J Biol Chem. 2014;289:1905–16.
Lin WH, Chiu KC, Chang HM, Lee KC, Tai TY, Chuang LM. Molecular scanning of the human sorbin and SH3-domain-containing-1 (SORBS1) gene: positive association of the T228A polymorphism with obesity and type 2 diabetes. Hum Mol Genet. 2001;10:1753–60.
Yang WS, Lee WJ, Huang KC, Lee KC, Chao CL, Chen CL, Tai TY, Chuang LM. MRNA levels of the insulin-signaling molecule SORBS1 in the adipose depots of nondiabetic women. Obes Res. 2003;11:586–90.
Brey CW, Nelder MP, Hailemariam T, Gaugler R, Hashmi S. Kruppel-like family of transcription factors: an emerging new frontier in fat biology. Int J Biol Sci. 2009;5:622–36.
Chen Z, Ding Z, Ma G, Liu N, Qian Q. Sterol regulatory element-binding transcription factor (SREBF)-2, SREBF cleavage-activating protein (SCAP), and premature coronary artery disease in a Chinese population. Mol Biol Rep. 2011;38:2895–901.
Verardo LL, Nascimento CS, Silva FF, Gasparino E, Martins MF, Toriyama E, Faria VR, Botelho ME, Costa KA, Lopes PS, et al. Identification and validation of differentially expressed genes from pig skeletal muscle. J Anim Breed Genet. 2013;130:372–81.
Kim SS, Kim JR, Moon JK, Choi BH, Kim TH, Kim KS, Kim JJ, Lee CK. Transcriptional alteration of p53 related processes as a key factor for skeletal muscle characteristics in Sus Scrofa. Mol Cells. 2009;28:565–73.
Ma W, Lu S, Sun T, Wang X, Ma Y, Zhang X, Zhao R, Wang Y. Twist 1 regulates the expression of PPARgamma during hormone-induced 3T3-L1 preadipocyte differentiation: a possible role in obesity and associated diseases. Lipids Health Dis. 2014;13:132.
Ren R, Chen Z, Zhao X, Sun T, Zhang Y, Chen J, Lu S, Ma W. A possible regulatory link between twist 1 and PPARgamma gene regulation in 3T3-L1 adipocytes. Lipids Health Dis. 2016;15:189.
Zhou J, Sears RL, Xing X, Zhang B, Li D, Rockweiler NB, Jang HS, Choudhary MNK, Lee HJ, Lowdon RF, et al. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. BMC Genomics. 2017;18:724.
Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, Reddy SU, Chandak GR, et al. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One. 2012;7:e31621.
Kass SU, Landsberger N, Wolffe AP. DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol. 1997;7:157–65.
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol. 2009;27:361–8.
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin SK, Rigoutsos I, Loring J, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20:320–31.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215–9.
Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006;31:89–97.
Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol. 2004;11:1068–75.
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92.
Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell. 2011;42:451–64.
Murad JM, Place CS, Ran C, Hekmatyar SKN, Watson NP, Kauppinen RA, Israel MA. Inhibitor of DNA binding 4 (ID4) regulation of adipocyte differentiation and adipose tissue formation in mice. J Biol Chem. 2010;285:24164–73.
Park KW, Waki H, Villanueva CJ, Monticelli LA, Hong C, Kang S, MacDougald OA, Goldrath AW, Tontonoz P. Inhibitor of DNA binding 2 is a small molecule-inducible modulator of peroxisome proliferator-activated receptor-gamma expression and adipocyte differentiation. Mol Endocrinol. 2008;22:2038–48.
Gil A, María Aguilera C, Gil-Campos M, Cañete R. Altered signalling and gene expression associated with the immune system and the inflammatory response in obesity. Brit. J Nutr. 2007;98:S121–6.
Fan C, Dong H, Yan K, Shen W, Wang C, Xia L, Zhan D, Qi K. Genome-wide screen of promoter methylation identifies novel markers in diet-induced obese mice. Nutr Hosp. 2014;30:42–52.
de Koning DJ, Janss LL, Rattink AP, van Oers PA, de Vries BJ, Groenen MA, van der Poel JJ, de Groot PN, Brascamp EW, van Arendonk JA. Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus Scrofa). Genetics. 1999;152:1679–90.
Gerbens F, Verburg FJ, Van Moerkerk HT, Engel B, Buist W, Veerkamp JH, Te PM. Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs. J Anim Sci. 2001;79:347–54.
Demirel G, Wachira AM, Sinclair LA, Wilkinson RG, Wood JD, Enser M. Effects of dietary n-3 polyunsaturated fatty acids, breed and dietary vitamin E on the fatty acids of lamb muscle, liver and adipose tissue. Br J Nutr. 2004;91:551–65.
Jiang YZ, Zhu L, Li XW, Si T. Evaluation of the Chinese indigenous pig breed Dahe and crossbred Dawu for growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid and amino acid composition. Animal. 2011;5:1485–92.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5.
Schachtschneider KM, Madsen O, Park C, Rund LA, Groenen MAM, Schook LB. Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model. BMC Genomics. 2015;16:743.
Schultz MD, Schmitz RJ, Ecker JR. Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 2012;28:583–5.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
Miron M, Woody OZ, Marcil A, Murie C, Sladek R, Nadon R. A methodology for global validation of microarray experiments. BMC Bioinformatics. 2006;7:333.