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

Volumn 92, Issue 7, 2014, Pages 2832-2845

  Ramayo Caldas, Y ^a,b,c   Fortes, M R S ^d   Hudson, N J ^a   Porto Neto, L R ^a   Bolormaa, S ^e   Barendse, W ^a   Kelly, M ^d   Moore, S S ^d   Goddard, M E ^e,f   Lehnert, S A ^a   Reverter, A ^a  

^a CSIRO   (Australia)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^d UNIVERSITY OF QUEENSLAND   (Australia)

^e Victorian Department of Primary Industries   (Australia)

^f UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Association weight matrix; Beef quality; Fat deposition; Genomewide association study; Marbling

Indexed keywords

FORKHEAD TRANSCRIPTION FACTOR; GENETIC MARKER; HEPATOCYTE NUCLEAR FACTOR 4; TRANSCRIPTION FACTOR;

ANATOMY AND HISTOLOGY; ANIMAL; BOVINE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC MARKER; GENETICS; MEAT; OBESITY; PHYSIOLOGY; QUANTITATIVE TRAIT; SKELETAL MUSCLE; STANDARDS; VETERINARY;

ADIPOSITY; ANIMALS; CATTLE; FORKHEAD TRANSCRIPTION FACTORS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; HEPATOCYTE NUCLEAR FACTOR 4; MEAT; MUSCLE, SKELETAL; QUANTITATIVE TRAIT, HERITABLE; TRANSCRIPTION FACTORS;

EID: 84905041405     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2013-7484     Document Type: Conference Paper

References (77)

1. Barendse, W. 2011. Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle. PLoS ONE 6:E29601.
2. Barendse, W., B. E. Harrison, R. J. Bunch, and M. B. Thomas. 2008. Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle. BMC Genet. 9:41
3. Barwick, S. A., D. J. Johnston, H. M. Burrow, R. G. Holroyd, G. Fordyce, M. L. Wolcott, W. D. Sim, and M. T. Sullivan. 2009a. Genetics of heifer performance in 'wet' and 'dry' seasons and their relationships with steer performance in two tropical beef genotypes. Anim. Prod. Sci. 49:367-382.
4. Barwick, S. A., M. L. Wolcott, D. J. Johnston, H. M. Burrow, and M. T. Sullivan. 2009b. Genetics of steer daily and residual feed intake in two tropical beef genotypes, and relationships among intake, body composition, growth and other post-weaning measures. Anim. Prod. Sci. 49:351-366.
5. Benjamini, Y. and Y. Hochberg. 1995. Controlling the false discovery rate - A practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57:289-300.
6. Berndt, S. I., S. Gustafsson, R. Maegi, A. Ganna, E. Wheeler, M. F. Feitosa, A. E. Justice, K. L. Monda, D. C. Croteau-Chonka, F. R. Day, T. Esko, T. Fall, T. Ferreira, D. Gentilini, A. U. Jackson, J. A. Luan, J. C. Randall, S. Vedantam, C. J. Willer, T. W. Winkler, A. R. Wood, T. Workalemahu, Y.-J. Hu, S. H. Lee, L. Liang, D.-Y. Lin, J. L. Min, B. M. Neale, G. Thorleifsson, J. Yang, E. Albrecht, N. Amin, J. L. Bragg-Gresham, G. Cadby, M. den Heijer, N. Eklund, K. Fischer, A. Goel, J.-J. Hottenga, J. E. Huffman, I. Jarick, A. Johansson, T. Johnson, S. Kanoni, M. E. Kleber, I. R. Koenig, K. Kristiansson, Z. Kutalik, C. Lamina, C. Lecoeur, G. Li, M. Mangino, W. L. McArdle, C. Medina-Gomez, M. Mueller-Nurasyid, J. S. Ngwa, I. M. Nolte, L. Paternoster, S. Pechlivanis, M. Perola, M. J. Peters, M. Preuss, L. M. Rose, J. Shi, D. Shungin, A. V. Smith, R. J. Strawbridge, I. Surakka, A. Teumer, M. D. Trip, J. Tyrer, J. V. Van Vliet-Ostaptchouk, L. Vandenput, L. L. Waite, J. H. Zhao, D. Absher, F. W. Asselbergs, M. Atalay, A. P. Attwood, A. J. Balmforth, H. Basart, J. Beilby, L. L. Bonnycastle, P. Brambilla, M. Bruinenberg, H. Campbell, D. I. Chasman, P. S. Chines, F. S. Collins, J. M. Connell, W. O. Cookson, U. de Faire, F. de Vegt, M. Dei, M. Dimitriou, S. Edkins, K. Estrada, D. M. Evans, M. Farrall, M. M. Ferrario, J. Ferrieres, L. Franke, F. Frau, P. V. Gejman, H. Grallert, H. Groenberg, V. Gudnason, A. S. Hall, P. Hall, A.-L. Hartikainen, C. Hayward, N. L. Heard-Costa, A. C. Heath, J. Hebebrand, G. Homuth, F. B. Hu, S. E. Hunt, E. Hyppoenen, C. Iribarren, K. B. Jacobs, J.-O. Jansson, A. Jula, M. Kahonen, S. Kathiresan, F. Kee, K.-T. Khaw, M. Kivimaki, W. Koenig, A. T. Kraja, M. Kumari, K. Kuulasmaa, J. Kuusisto, J. H. Laitinen, T. A. Lakka, C. Langenberg, L. J. Launer, L. Lind, J. Lindstrom, J. Liu, A. Liuzzi, M.-L. Lokki, M. Lorentzon, P. A. Madden, P. K. Magnusson, P. Manunta, D. Marek, W. Maerz, I. M. Leach, B. McKnight, S. E. Medland, E. Mihailov, L. Milani, G. W. Montgomery, V. Mooser, T. W. Muehleisen, P. B. Munroe, A. W. Musk, N. Narisu, G. Navis, G. Nicholson, E. A. Nohr, K. K. Ong, B. A. Oostra, C. N. A. Palmer, A. Palotie, J. F. Peden, N. Pedersen, A. Peters, O. Polasek, A. Pouta, P. P. Pramstaller, I. Prokopenko, C. Puetter, A. Radhakrishnan, O. Raitakari, A. Rendon, F. Rivadeneira, I. Rudan, T. E. Saaristo, J. G. Sambrook, A. R. Sanders, S. Sanna, J. Saramies, S. Schipf, S. Schreiber, H. Schunkert, S.-Y. Shin, S. Signorini, J. Sinisalo, B. Skrobek, N. Soranzo, A. Stancakova, K. Stark, J. C. Stephens, K. Stirrups, R. P. Stolk, M. Stumvoll, A. J. Swift, E. V. Theodoraki, B. Thorand, D.-A. Tregouet, E. Tremoli, M. M. Van der Klauw, J. B. J. van Meurs, S. H. Vermeulen, J. Viikari, J. Virtamo, V. Vitart, G. Waeber, Z. Wang, E. Widen, S. H. Wild, G. Willemsen, B. R. Winkelmann, J. C. M. Witteman, B. H. R. Wolffenbuttel, A. Wong, A. F. Wright, M. C. Zillikens, P. Amouyel, B. O. Boehm, E. Boerwinkle, D. I. Boomsma, M. J. Caulfield, S. J. Chanock, L. A. Cupples, D. Cusi, G. V. Dedoussis, J. Erdmann, J. G. Eriksson, P. W. Franks, P. Froguel, C. Gieger, U. Gyllensten, A. Hamsten, T. B. Harris, C. Hengstenberg, A. A. Hicks, A. Hingorani, A. Hinney, A. Hofman, K. G. Hovingh, K. Hveem, T. Illig, M.-R. Jarvelin, K.- H. Joeckel, S. M. Keinanen-Kiukaanniemi, L. A. Kiemeney, D. Kuh, M. Laakso, T. Lehtimaki, D. F. Levinson, N. G. Martin, A. Metspalu, A. D. Morris, M. S. Nieminen, I. Njolstad, C. Ohlsson, A. J. Oldehinkel, W. H. Ouwehand, L. J. Palmer, B. Penninx, C. Power, M. A. Province, B. M. Psaty, L. Qi, R. Rauramaa, P. M. Ridker, S. Ripatti, V. Salomaa, N. J. Samani, H. Snieder, T. I. A. Sorensen, T. D. Spector, K. Stefansson, A. Tonjes, J. Tuomilehto, A. G. Uitterlinden, M. Uusitupa, P. van der Harst, P. Vollenweider, H. Wallaschofski, N. J. Wareham, H. Watkins, H. E. Wichmann, J. F. Wilson, G. R. Abecasis, T. L. Assimes, I. Barroso, M. Boehnke, I. B. Borecki, P. Deloukas, C. S. Fox, T. Frayling, L. C. Groop, T. Haritunian, I. M. Heid, D. Hunter, R. C. Kaplan, F. Karpe, M. F. Moffatt, K. L. Mohlke, J. R. O'Connell, Y. Pawitan, E. E. Schadt, D. Schlessinger, V. Steinthorsdottir, D. P. Strachan, U. Thorsteinsdottir, C. M. van Duijn, P. M. Visscher, A. M. Di Blasio, J. N. Hirschhorn, C. M. Lindgren, A. P. Morris, D. Meyre, A. Scherag, M. I. McCarthy, E. K. Speliotes, K. E. North, R. J. F. Loos, and E. Ingelsson. 2013. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat. Genet. 45:501-512.
7. Berridge, M. J., P. Lipp, and M. D. Bootman. 2000. The versatility and universality of calcium signalling. Nat. Rev. Mol. Cell Biol. 1:11-21.
8. Boj, S. F., M. Parrizas, M. A. Maestro, and J. Ferrer. 2001. A transcription factor regulatory circuit in differentiated pancreatic cells. Proc. Natl. Acad. Sci. USA 98:14481-14486.
9. Bolormaa, S., B. J. Hayes, K. Savin, R. Hawken, W. Barendse, P. F. Arthur, R. M. Herd, and M. E. Goddard. 2011a. Genomewide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89:1684-1697.
10. Bolormaa, S., L. R. Neto, Y. D. Zhang, R. J. Bunch, B. E. Harrison, M. E. Goddard, and W. Barendse. 2011b. A genome-wide association study of meat and carcass traits in Australian cattle. J. Anim. Sci. 89:2297-2309.
11. Bolormaa, S., J. E. Pryce, K. Kemper, K. Savin, B. J. Hayes, W. Barendse, Y. Zhang, C. M. Reich, B. A. Mason, R. J. Bunch, B. E. Harrison, A. Reverter, R. M. Herd, B. Tier, H. U. Graser, and M. E. Goddard. 2013. Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. J. Anim. Sci. 91:3088-3104.
12. Bolormaa, S., J. E. Pryce, A. Reverter, Y. Zhang, W. Barendse, K. Kemper, B. Tier, K. Savin, B. J. Hayes, and M. E. Goddard. 2014. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genet. 10:E1004198.
13. Browning, B. L., and S. R. Browning. 2011. A fast, powerful method for detecting identity by descent. Am. J. Hum. Genet. 88:173-182.
14. Calvano, S. E., W. Z. Xiao, D. R. Richards, R. M. Felciano, H. V. Baker, R. J. Cho, R. O. Chen, B. H. Brownstein, J. P. Cobb, S. K. Tschoeke, C. Miller-Graziano, L. L. Moldawer, M. N. Mindrinos, R. W. Davis, R. G. Tompkins, S. F. Lowry, and I. H. R. Injury. 2005. A network-based analysis of systemic inflammation in humans. Nature 437:1032-1037.
15. Cao, X. and Y. Chen. 2009. Mitochondria and calcium signaling in embryonic development. Semin. Cell Dev. Biol. 20:337-345.
16. Cipolletta, D., M. Feuerer, A. Li, N. Kamei, J. Lee, S. E. Shoelson, C. Benoist, and D. Mathis. 2012. PPAR-gamma is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature 486:549-553.
17. De Smet, S., K. Raes, and D. Demeyer. 2004. Meat fatty acid composition as affected by fatness and genetic factors: A review. Anim. Res. 53:81-98.
18. Dear, T. N., and T. Boehm. 1999. Diverse mRNA expression patterns of the mouse calpain genes Capn5, Capn6 and Capn11 during development. Mech. Dev. 89:201-209.
19. Drewes, T., S. Senkel, B. Holewa, and G. U. Ryffel. 1996. Human hepatocyte nuclear factor 4 isoforms are encoded by distinct and differentially expressed genes. Mol. Cell. Biol. 16:925-931.
20. Eloranta, J. J., and G. A. Kullak-Ublick. 2005. Coordinate transcriptional regulation of bile acid homeostasis and drug metabolism. Arch. Biochem. Biophys. 433:397-412.
21. Esterbauer, H., H. Oberkofler, V. Linnemayr, B. Iglseder, M. Hedegger, P. Wolfsgruber, B. Paulweber, G. Fastner, F. Krempler, and W. Patsch. 2002. Peroxisome proliferator-activated receptor- gamma coactivator-1 gene locus: Associations with obesity indices in middle-aged women. Diabetes 51:1281-1286.
22. Feuerer, M., L. Herrero, D. Cipolletta, A. Naaz, J. Wong, A. Nayer, J. Lee, A. B. Goldfine, C. Benoist, S. Shoelson, and D. Mathis. 2009. Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters. Nat. Med. 15:930-939.
23. Fortes, M. R. S., A. Reverter, S. H. Nagaraj, Y. Zhang, N. N. Jonsson, W. Barris, S. Lehnert, G. B. Boe-Hansen, and R. J. Hawken. 2011. A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle. J. Anim. Sci. 89:1669-1683.
24. Fortes, M. R. S., A. Reverter, Y. Zhang, E. Collis, S. H. Nagaraj, N. N. Jonsson, K. C. Prayaga, W. Barris, and R. J. Hawken. 2010. Association weight matrix for the genetic dissection of puberty in beef cattle. Proc. Natl. Acad. Sci. USA 107:13642-13647.
25. Garnier, J. P., R. Klont, and G. Plastow. 2003. The potential impact of current animal research on the meat industry and consumer attitudes towards meat. Meat Sci. 63:79-88.
26. Gerdin, A. K., V. V. Surve, M. Jonsson, M. Bjursell, M. Bjorkman, A. Edenro, M. Schuelke, A. Saad, S. Bjurstrom, E. J. Lundgren, M. Snaith, R. Fransson-Steen, J. Tornell, A.-L. Berg, and M. Bohlooly-Y. 2006. Phenotypic screening of hepatocyte nuclear factor (HNF) 4-gamma receptor knockout mice. Biochem. Biophys. Res. Commun. 349:825-832.
27. Gilmour, A., B. Gogel, B. Cullis, S. Welham, and R. Thompson. 2002. ASReml user guide release 1.0. VSN International Ltd., Hemel Hempstead, UK.
28. Hara, K., K. Tobe, T. Okada, H. Kadowaki, Y. Akanuma, C. Ito, S. Kimura, and T. Kadowaki. 2002. A genetic variation in the PGC-1 gene could confer insulin resistance and susceptibility to Type II diabetes. Diabetologia 45:740-743.
29. Harper, G. S., and D. W. Pethick. 2004. How might marbling begin? Aust. J. Exp. Agric. 44:653-662.
30. Horii, M., Y. Sakurai, Y. Kanbe, K. Kasai, T. Asada, M. Kobayashi, M. Yamada, M. Hayashi, and K. Hodate. 2009. Relationship between Japanese Beef Marbling Standard numbers and intramuscular lipid in M. longissimus thoracis of Japanese Black steers from 1996 to 2004. Anim. Sci. J. 80:55-61.
31. Hudson, N. J., R. E. Lyons, A. Reverter, P. L. Greenwood, and B. P. Dalrymple. 2013. Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data. Gene Expr. Patterns 13:109-125.
32. Ichida, M., S. Nemoto, and T. Finkel. 2002. Identification of a specific molecular repressor of the peroxisome proliferator-activated receptor gamma Coactivator-1 alpha (PGC-1alpha). J. Biol. Chem. 277:50991-50995.
33. Johnston, D. J., A. Reverter, H. M. Burrow, V. H. Oddy, and D. L. Robinson. 2003a. Genetic and phenotypic characterisation of animal, carcass, and meat quality traits from temperate and tropically adapted beef breeds. 1. Animal measures. Aust. J. Agric. Res. 54:107-118.
34. Johnston, D. J., A. Reverter, D. M. Ferguson, J. M. Thompson, and H. M. Burrow. 2003b. Genetic and phenotypic characterisation of animal, carcass, and meat quality traits from temperate and tropically adapted beef breeds. 3. Meat quality traits. Aust. J. Agric. Res. 54:135-147.
35. Johnston, J., Y. Ramos-Valdes, L.-A. Stanton, S. Ladhani, F. Beier, and G. E. DiMattia. 2010. Human stanniocalcin-1 or-2 expressed in mice reduces bone size and severely inhibits cranial intramembranous bone growth. Transgenic Res. 19:1017-1039.
36. Kerry, J. P., and D. Ledward. 2009. Improving the sensory and nutritional quality of fresh meat. Woodhead Publishing, Sawston, Cambridge, UK.
37. Kim, C. H. 2009. FOXP3 and its role in the immune system. Adv. Exp. Med. Biol. 665:17-29.
38. Komisarek, J. and A. Walendowska. 2012. Analysis of the PPARGC1A gene as a potential marker for productive and reproductive traits in cattle. Folia Biol. (Krakow) 60:171-174.
39. Liu, R. R., Y. F. Sun, G. P. Zhao, F. J. Wang, D. Wu, M. Q. Zheng, J. L. Chen, L. Zhang, Y. D. Hu, and J. Wen. 2013. Genome-wide association study identifies loci and candidate genes for body composition and meat quality traits in Beijing-You chickens. PLoS ONE 8:E61172.
40. Menssen, A., T. Haeupl, M. Sittinger, B. Delorme, P. Charbord, and J. Ringe. 2011. Differential gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenic development. BMC Genomics 12:461.
41. Moloney, A. P., M. T. Mooney, J. P. Kerry, C. Stanton, and P. O'Kiely. 2013. Colour of fat, and colour, fatty acid composition and sensory characteristics of muscle from heifers offered alternative forages to grass silage in a finishing ration. Meat Sci. 95:608-615.
42. Pacifici, R. 2010. T cells: Critical bone regulators in health and disease. Bone 47:461-471.
43. Parnell, P. F. 2004. Industry application of marbling genetics: A brief review. Aust. J. Exp. Agric. 44:697-703.
44. Pena, R. N., J. L. Noguera, J. Casellas, I. Diaz, A. I. Fernandez, J. M. Folch, and N. Ibanez-Escriche. 2013. Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim. Genet. 44:648-660.
45. Perry, D., W. R. Shorthose, D. M. Ferguson, and J. M. Thompson. 2001. Methods used in the CRC program for the determination of carcass yield and beef quality. Aust. J. Exp. Agric. 41:953-957.
46. Peters, S. O., K. Kizilkaya, D. J. Garrick, R. L. Fernando, J. M. Reecy, R. L. Weaber, G. A. Silver, and M. G. Thomas. 2012. Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers. J. Anim. Sci. 90:3398-3409.
47. Porto Neto, L. R., R. J. Bunch, B. E. Harrison, and W. Barendse. 2012. Variation in the XKR4 gene was significantly associated with subcutaneous rump fat thickness in indicine and composite cattle. Anim. Genet. 43:785-789.
48. Ramayo-Caldas, Y., M. Ballester, M. R. Fortes, A. Esteve-Codina, A. Castello, J. L. Noguera, A. I. Fernandez, M. Perez-Enciso, A. Reverter, and J. M. Folch. 2014. From SNP co-association to RNA co-expression: Novel insights into gene networks for intramuscular fatty acid composition in porcine. BMC Genomics 15:232.
49. Ramayo-Caldas, Y., A. Mercade, A. Castello, B. Yang, C. Rodriguez, E. Alves, I. Diaz, N. Ibanez-Escriche, J. L. Noguera, M. Perez- Enciso, A. I. Fernandez, and J. M. Folch. 2012. Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross. J. Anim. Sci. 90:2883-2893.
50. Reverter, A. and E. K. F. Chan. 2008. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics 24:2491-2497.
51. Reverter, A. and M. R. Fortes. 2013a. Association weight matrix: A network-based approach towards functional genome-wide association studies. Methods Mol. Biol. 1019:437-447.
52. Reverter, A. and M. R. S. Fortes. 2013b. Breeding and genetics symposium: Building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies. J. Anim. Sci. 91:530-536.
53. Reverter, A., D. J. Johnston, D. M. Ferguson, D. Perry, M. E. Goddard, H. M. Burrow, V. H. Oddy, J. M. Thompson, and B. M. Bindon. 2003a. Genetic and phenotypic characterisation of animal, carcass, and meat quality traits from temperate and tropically adapted beef breeds. 4. Correlations among animal, carcass, and meat quality traits. Aust. J. Agric. Res. 54:149-158.
54. Reverter, A., D. J. Johnston, D. Perry, M. E. Goddard, and H. M. Burrow. 2003b. Genetic and phenotypic characterisation of animal, carcass, and meat quality traits from temperate and tropically adapted beef breeds. 2. Abattoir carcass traits. Aust. J. Agric. Res. 54:119-134.
55. Rhee, J., Y. Inoue, J. C. Yoon, P. Puigserver, M. L. Fan, F. J. Gonzalez, and B. M. Spiegelman. 2003. Regulation of hepatic fasting response by PPAR gamma coactivator-1 alpha (PGC-1): Requirement for hepatocyte nuclear factor 4 alpha in gluconeogenesis. Proc. Natl. Acad. Sci. USA 100:4012-4017.
56. Rudensky, A. Y. 2011. Regulatory T cells and Foxp3. Immunol. Rev. 241:260-268.
57. Scardoni, G., M. Petterlini, and C. Laudanna. 2009. Analyzing biological network parameters with CentiScaPe. Bioinformatics 25:2857-2859.
58. Sevane, N., E. Armstrong, O. Cortes, P. Wiener, R. P. Wong, and S. Dunner. 2013. Association of bovine meat quality traits with genes included in the PPARG and PPARGC1A networks. Meat Sci. 94:328-335.
59. Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-2504.
60. Shin, S. and E. Chung. 2013. Novel SNPs in the bovine ADIPOQ and PPARGC1A genes are associated with carcass traits in Hanwoo (Korean cattle). Mol. Biol. Rep. 40:4651-4660.
61. Snelling, W. M., R. A. Cushman, J. W. Keele, C. Maltecca, M. G. Thomas, M. R. S. Fortes, and A. Reverter. 2013. Breeding and genetics symposium: Networks and pathways to guide genomic selection. J. Anim. Sci. 91:537-552.
62. Stoffel, M. and S. A. Duncan. 1997. The maturity-onset diabetes of the young (MODY1) transcription factor HNF4 alpha regulates expression of genes required for glucose transport and metabolism. Proc. Natl. Acad. Sci. USA 94:13209-13214.
63. Summermatter, S., G. Shui, D. Maag, G. Santos, M. R. Wenk, and C. Handschin. 2013. PGC-1alpha improves glucose homeostasis in skeletal muscle in an activity-dependent manner. Diabetes 62:85-95.
64. Sun, W., N. J. Hudson, A. Reverter, A. J. Waardenberg, R. L. Tellam, T. Vuocolo, K. Byrne, and B. P. Dalrymple. 2012. An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape. BMC Res. Notes 5:632.
65. Taraviras, S., T. Mantamadiotis, T. Dong-Si, A. Mincheva, P. Lichter, T. Drewes, G. U. Ryffel, A. P. Monaghan, and G. Schutz. 2000. Primary structure, chromosomal mapping, expression and transcriptional activity of murine hepatocyte nuclear factor 4 gamma. Biochim. Biophys. Acta 1490:21-32.
66. Tizioto, P. C., J. E. Decker, J. F. Taylor, R. D. Schnabel, M. A. Mudadu, F. L. Silva, G. B. Mourao, L. L. Coutinho, P. Tholon, T. S. Sonstegard, A. N. Rosa, M. M. Alencar, R. R. Tullio, S. R. Medeiros, R. T. Nassu, G. L. Feijo, L. O. Silva, R. A. Torres, F. Siqueira, R. H. Higa, and L. C. Regitano. 2013. Genome scan for meat quality traits in Nelore beef cattle. Physiol. Genomics 45:1012-1020.
67. Tizioto, P. C., S. L. Meirelles, R. R. Tulio, A. N. Rosa, M. M. Alencar, S. R. Medeiros, F. Siqueira, G. L. D. Feijo, L. O. C. Silva, R. A. A. Torres, and L. C. A. Regitano. 2012. Candidate genes for production traits in Nelore beef cattle. Genet. Mol. Res. 11:4138-4144.
68. Tonami, K., S. Hata, K. Ojima, Y. Ono, Y. Kurihara, T. Amano, T. Sato, Y. Kawamura, H. Kurihara, and H. Sorimachi. 2013. Calpain- 6 deficiency promotes skeletal muscle development and regeneration. PLoS Genet. 9:E1003668.
69. Upton, W., H. M. Burrow, A. Dundon, D. L. Robinson, and E. B. Farrell. 2001. CRC breeding program design, measurements and database: Methods that underpin CRC research results. Aust. J. Exp. Agric. 41:943-952.
70. van Amerongen, R., and R. Nusse. 2009. Towards an integrated view of Wnt signaling in development. Development 136:3205-3214.
71. Wang, Y. H., K. A. Byrne, A. Reverter, G. S. Harper, M. Taniguchi, S. M. McWilliam, H. Mannen, K. Oyama, and S. A. Lehnert. 2005. Transcriptional profiling of skeletal muscle tissue from two breeds of cattle. Mamm. Genome 16:201-210.
72. Warner, R. D., P. L. Greenwood, D. W. Pethick, and D. M. Ferguson. 2010. Genetic and environmental effects on meat quality. Meat Sci. 86:171-183.
73. Wisely, G. B., A. B. Miller, R. G. Davis, A. D. Thornquest Jr., R. Johnson, T. Spitzer, A. Sefler, B. Shearer, J. T. Moore, A. B. Miller, T. M. Willson, and S. P. Williams. 2002. Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids. Structure 10:1225-1234.
74. Yamada, T., S. Sasaki, S. Sukegawa, T. Miyake, T. Fujita, H. Kose, M. Morita, Y. Takahagi, H. Murakami, F. Morimatsu, and Y. Sasaki. 2009. Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle. Anim. Sci. J. 80:486-489.
75. Yang, J., B. Benyamin, B. P. McEvoy, S. Gordon, A. K. Henders, D. R. Nyholt, P. A. Madden, A. C. Heath, N. G. Martin, G. W. Montgomery, M. E. Goddard, and P. M. Visscher. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42:565-569.
76. Yoneda, M., K. Hotta, Y. Nozaki, H. Endo, T. Uchiyama, H. Mawatari, H. Iida, S. Kato, K. Hosono, K. Fujita, K. Yoneda, H. Takahashi, H. Kirikoshi, N. Kobayashi, M. Inamori, Y. Abe, K. Kubota, S. Saito, S. Maeyama, K. Wada, and A. Nakajima. 2008. Association between PPARGC1A polymorphisms and the occurrence of nonalcoholic fatty liver disease (NAFLD). BMC Gastroenterol. 8:27.
77. Zhao, C., F. Tian, Y. Yu, J. Luo, A. Mitra, F. Zhan, Y. Hou, G. Liu, L. Zan, M. S. Updike, and J. Song. 2012. Functional genomic analysis of variation on beef tenderness induced by acute stress in Angus cattle. Comp. Funct. Genomics 2012:1.