Identification of Functional and In silico Positional Differentially Expressed Genes in the Livers of High- and Low-marbled Hanwoo Steers

  • Lee, Seung-Hwan (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Park, Eung-Woo (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Cho, Yong-Min (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Yoon, Duhak (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Park, Jun-Hyung (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Hong, Seong-Koo (Nutrition & Physiology Division, National Institute of Animal Science, RDA) ;
  • Im, Seok-Ki (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Thompson, J.M. (The Cooperative Research Centre for Beef Genetic Technologies, The University of New England) ;
  • Oh, Sung-Jong (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA)
  • Received : 2006.11.06
  • Accepted : 2007.04.07
  • Published : 2007.09.01


This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.


  1. Bauchart, D. 1993. Lipid apsorption and transport in ruminants. J. Dairy Sci. 76:3864-3881
  2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215(3):403-410
  3. Florini, J. R., D. Z. Ewton and S. A. Coolican. 1996. Growth hormone and the insulin-like growth factor system in myogenesis. Endocr. Rev. 17:481-517
  4. Fernando, M.-S., S. Wilkens and J. J. Garcia. 2005. Structure of dimeric mitochondrial ATP synthase: novel F0 bridging features and the structural basis of mitochondrial cristae biogenesis. Proc. Natl. Acad. Sci. USA. 102:12356-12358
  5. Briles, W. E. 1954. Evidence of overdominance of the B blood group alleles in the chicken. Genet. 39:961-965
  6. Chen, Q., S. Wang, S. N. Thompson, E. D. Hall and R. P. Guttmann. 2006. Identification and characterization of PEBP as a calpain substrate. J. Neurochem. 99:1133-1138
  7. Gromada, J. C., K. Bark, A. M. Smidt, J. Efanov, S. A. Janson, D. Mandic, W. Webb, B. Zhang, A. Meister, Jeromin and P-O. Berggren. 2005. Neuronal calcium sensor-1 potentiates glucose-dependent exocytosis in pancreatic b cells through activation of phosphatidylinositol 4-kinase beta. Proc. Natl. Acad. Sci. USA. 102:10303-10308
  8. Grum, D. E., J. K. Drackley and J. H. Clark. 2002. Fatty acid metabolism in liver of dairy cows fed supplemental fat and nicotinic acid during an entire lactation. J. Dairy Sci. 85:3026-3034
  9. Gehrmann, T. and L. M. G. Heilmeyer. 1998. Phosphatidylinositol 4-kinases. Eur. J. Biochem. 253:357-370
  10. Hwang, In-Tak, Yun-Jee Kim, Seung Hyun Kim, Chae-il Kwak, Young-Yun Gu and Jong-Yoon Chun. 2003. Annealing control primer system for improving specificity of PCR amplification. BioTechniques 35:1180-1184
  11. Hinokio, Y., S. Suzuki, K. Komatu, M. Ohtomo, M. Onoda, M. Matsumoto, S. Hirai, Y. Sato, H. Akai and K. Abe. 1995. A new mitochondrial DNA deletion associated with diabetic amyotrophy, diabetic myoatrophy and diabetic fatty liver. Muscle Nerve. 3:S142-149
  12. Hayward, B. E., J. A. Fantes, J. P. Warner, S. Intody, J. P. Leek, A. F. Markham and D. T. Bonthron. 1996. Co-localization of the ketohexokinase and glucokinase regulator genes to a 500-kb region of chromosome 2p23. Mamm Genome. 7:454-458
  13. Kim, C. J. and E. S. Lee. 2003. Effects of quality grade on the chemical, physical and sensory characteristics of Hanwoo (Korean native cattle) beef. Meat Sci. 63:397-405
  14. Jung, Y. C., M. F. Rothchild, M. P. Flanagan, L. Christian and C. M. Warner. 1989. Association of restriction fragment length polymorphisms of swine leukocyte antigen class I genes with production traits of Duroc and Hampshire boars. Anim. Genet. 20(1):79-91
  15. Kappes, S. M., J. W. Keele, R. T. Stone, R. A. McGraw, T. S. Sonstegard, T. P. Smith, N. L. Lopez-Corrales and C. W. Beattie. 1997. A second-generation linkage map of the bovine genome. Genome. Res. 7(3):235-249
  16. JMGA. 1988. New beef carcass grading standards. Japan Meat Grading Association, Tokyo, Japan
  17. Kim, Yun-Jee, Chae-iI Kwak, Young-Yun Gu, In-Taek Hwang and Jong-Yoon Chun. 2004. Annealing control primer system for identification of differentially expressed genes on agarose gels. BioTechniques 36:424-434
  18. Lee, H. C., B. Tian, J. M. Sedivy, J. R. Wands and M. Kim. 2006. Loss of raf kinase inhibitor protein promotes cell proliferation and migration of human hepatoma cells. Gastroenterol. 131:1208-1217
  19. Kim, J. Y., D. H. Yoon, B. L. Park, L. H. Kim, K. J. Na, J. G. Choi, C. Y. Cho, J. K. Lee, E. R. Chung, B. C. Sang, I. J. Cheong, S. J. Oh and H. D. Shin. 2005. Identification of novel SNPs in bovine insulin-like growth factor binding protein-3 (IGFBP3) gene. Asian-Aust. J. Anim. Sci. 18(1):3-7
  20. Nicoletti, V. G., V. M. Marino, C. Cuppari, D. Licciardello, D. Patti, V. S. Purrello and A. M. Stella. 2005. Effect of antioxidant diets on mitochondrial gene expression in rat brain during aging. Neurochem Res. 30:737-752
  21. Min, J., S. Okada, M. Kanzaki, J. Elmendorf, K. Coker, B. Ceresa, L. Syu, Y. Noda, A. Saltiel and J. S. Pessin. 1999. A novel insulin-regulated syntaxin 4-binding protein mediating GLUT4 translocation in adipocytes. Molecular. Cell. 3:751-760
  22. Lee, H. G., H. Hidari, S. K Kang, Z. S. Hong, C. X. Xu, S. H. Kim, K. S. Seo, D. H. Yoon and Y. J. Choi. 2005. The relationships between plasma insulin-like growth factor (IGF)-1 and IGFbinding proteins (IGFBPs) to growth pattern, and characteristics of plasma IGFBPs in steers. Asian-Aust. J. Anim. Sci. 18(11):1575-1581
  23. Ponsuksili, S., E. Murani, K. Schellander, M. Schwerin and K. Wimmers. 2005. Identification of functional candidate genes for body composition by expression analyses and evidencing impact by association analysis and mapping. Biochimica et Biophysica Acta 1730:31-40
  24. Wimmers, K., S. Mekchay, K. Schellander and S. Ponsuksili. 2003. Molecular characterization of the pig C3 gene and its association with complement activity. Immunogenetics. 54: 714-724
  25. USDA. 1989. Official united states standards for grades of beef carcases. Agric. Marketing Serv. USDA, Washington, DC
  26. Simpson, E., G. Bulfield, M. Brenan, W. Fitzpatrick, C. Hetherington and A. Blann. 1982. H-2 associated differences in replocated strains of mice divergently selected for body weight. Immunogenetics 15:63-70
  27. Kim, J. H., B. H Choi, H. T. Lim, E. W. Park, S. H. Lee, B. Y. Seo, I. C. Cho, J. G. Lee, S. J. Oh and J. T. Jeon. 2005. Characterization of phosphoinositide-3-kinase, class 3 (PIK3C3) gene and association tests with quantitative traits in pigs. Asian-Aust. J. Anim. Sci. 18:1701-1707
  28. Wang, Y. H., A. B. Keren, 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
  29. Jones, J. I. and D. R. Clemmons. 1995. Insulin-like growth factor binding protein: biological action. Endocr. Rev. 16(1):3-34
  30. Childs, K. D., D. W. Goad, M. F. Allan, D. Pomp, C. Krehbiel, R. D. Geisert, J. B. Morgan and J. R. Malayer. 2002. Differential expression of NAT1 translational repressor during development of bovine intramuscular adipocytes. Physiol. Genomics 10:49-56