Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo

Kim, Seung-Chang;Lee, Seung-Hwan;Lee, Ji-Woong;Kim, Tae-Hun;Choi, Bong-Hwan

  • Received : 2014.10.18
  • Accepted : 2015.06.15
  • Published : 2016.01.01


The Fas (APO-1, TNFRSF6) gene known as a member of the tumor necrosis factor receptor superfamily was selected for DNA marker development in Korean cattle. It is a cell membrane protein and mediates programmed cell death (apoptosis). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers related to economical traits at the genomic level. The sequences of whole exon and 1 kb range of both front and back of the gene were determined by direct-sequencing methods using 24 cattle. A total of 55 SNPs were discovered and we selected 31 common polymorphic sites considering their allele frequencies, haplotype-tagging status and linkage disequilibrium (LD) for genotyping in larger-scale subjects. The SNPs were confirmed genotype through the SNaPshot method (n = 274) and were examined for a possible genetic association between Fas polymorphisms and marbling score. So, the SNPs that were identified significant are g.30256G>C, g.31474C>A, g.31940A>G, and g.32982G>A. These results suggest that SNPs of Fas gene were associated with intramuscular fat content of meat quality traits in Korean cattle.


Fas;Hanwoo;Linkage Disequilibrium;Marbling Score;Single Nucleotide Polymorphism


  1. APGS. 1995. Report of Business for Animal Products Grading. Animal Products Grading System, National Co-Operatives Federation, Korea.
  2. Bourdon, V., A. Harvey, and D. M. Lonsdale. 2001. Introns and their positions affect the translational activity of mrna in plant cells. EMBO Rep. 2:394-398.
  3. Buchman, A. R. and P. Berg. 1988. Comparison of intron-dependent and intron-independent gene expression. Mol. Cell Biol. 8:4395-4405.
  4. Callis, J., M. Fromm, and V. Walbot. 1987. Introns increase gene expression in cultured maize cells. Genes Dev. 1:1183-1200.
  5. Camerini, D., G. Walz, W. A. Loenen, J. Borst, and B. Seed. 1991. The T cell activation antigen cd27 is a member of the nerve growth factor/tumor necrosis factor receptor gene family. J Immunol. 147:3165-3169.
  6. Casas, E., J. W. Keele, S. D. Shackelford, M. Koohmaraie, and R. T. Stone. 2004. Identification of quantitative trait loci for growth and carcass composition in cattle. Anim. Genet. 35:2-6.
  7. Chiou, H. C., C. Dabrowski, and J. C. Alwine. 1991. Simian virus 40 late mRNA leader sequences involved in augmenting mRNA accumulation via multiple mechanisms, including increased polyadenylation efficiency. J. Virol. 65:6677-6685.
  8. Darvasi, A. and M. Soller. 1994. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138:1365-1373.
  9. Duncker, B. P., P. L. Davies, and V. K. Walker. 1997. Introns boost transgene expression in drosophila melanogaster. Mol. Gen. Genet. 254:291-296.
  10. Gautier, M., R. R. Barcelona, S. Fritz, C. Grohs, T. Druet, D. Boichard, A. Eggen, and T. H. Meuwissen. 2006. Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26. Genetics 172:425-436.
  11. Gill, J. L., S. C. Bishop, C. McCorquodale, J. L. Williams, and P. Wiener. 2010. Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial angus-cross population. Meat Sci. 86:985-993.
  12. Gilmour, A. R., B. J. Gogel, B. R. Cullis, and R. Thompson. 2006. Asreml User Guide Release 2.0. VSN International Ltd., Hempstead, HP1 1ES, UK.
  13. Gutierrez-Gil, B., P. Wiener, G. R. Nute, D. Burton, J. L. Gill, J. D. Wood, and J. L. Williams. 2008. Detection of quantitative trait loci for meat quality traits in cattle. Anim. Genet. 39:51-61.
  14. Itoh, N., S. Yonehara, A. Ishii, M. Yonehara, S. Mizushima, M. Sameshima, A. Hase, Y. Seto, and S. Nagata. 1991. The polypeptide encoded by the cdna for human cell surface antigen fas can mediate apoptosis. Cell 66:233-243.
  15. JMGA. 1988. New Beef Carcass Grading Standards. Japan Meat Grading Association, Tokyo, Japan.
  16. Johnson, D., A. Lanahan, C. R. Buck, A. Sehgal, C. Morgan, E. Mercer, M. Bothwell, and M. Chao. 1986. Expression and structure of the human NGF receptor. Cell 47:545-554.
  17. Kim, N. K., D. Lim, S. H. Lee, Y. M. Cho, E. W. Park, C. S. Lee, B. S. Shin, T. H. Kim, and D. Yoon. 2011. Heat shock protein B1 and its regulator genes are negatively correlated with intramuscular fat content in the longissimus thoracis muscle of hanwoo (Korean Cattle) steers. J Agric. Food Chem. 59:5657-5664.
  18. Lande, R. and R. Thompson. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743-756.
  19. Loetscher, H., Y. C. Pan, H. W. Lahm, R. Gentz, M. Brockhaus, H. Tabuchi, and W. Lesslauer. 1990. Molecular cloning and expression of the human 55 kd tumor necrosis factor receptor. Cell 61:351-359.
  20. Maj, A., J. Oprzadek, E. Dymnicki, and L. Zwierzchowski. 2006. Association of the polymorphism in the 5'-noncoding region of the bovine growth hormone receptor gene with meat production traits in Polish Black-and-White cattle. Meat Sci. 72:539-544.
  21. Mallett, S., S. Fossum, and A. N. Barclay. 1990. Characterization of the MRC OX40 antigen of activated CD4 positive T lymphocytes--a molecule related to nerve growth factor receptor. EMBO J. 9:1063-1068.
  22. Marques, E., J. D. Nkrumah, E. L. Sherman, and S. S. Moore. 2009. Polymorphisms in positional candidate genes on BTA14 and BTA26 affect carcass quality in beef cattle. J. Anim. Sci. 87:2475-2484.
  23. Miller, S. A., D. D. Dykes, and H. F. Polesky. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1215.
  24. Nott, A., S. H. Meislin, and M. J. Moore. 2003. A quantitative analysis of intron effects on mammalian gene expression. RNA 9:607-617.
  25. Oehm, A., I. Behrmann, W. Falk, M. Pawlita, G. Maier, C. Klas, M. Li-Weber, S. Richards, J. Dhein, and B. C. Trauth. 1992. Purification and molecular cloning of the APO-1 cell surface antigen, a member of the tumor necrosis factor/nerve growth factor receptor superfamily. Sequence identity with the Fas antigen. J. Biol. Chem. 267:10709-10715.
  26. Otto, G., R. Roehe, H. Looft, L. Thoelking, P. W. Knap, M. F. Rothschild, G. S. Plastow, and E. Kalm. 2007. Associations of DNA markers with meat quality traits in pigs with emphasis on drip loss. Meat Sci. 75:185-195.
  27. Palmiter, R. D., E. P. Sandgren, M. R. Avarbock, D. D. Allen, and R. L. Brinster. 1991. Heterologous introns can enhance expression of transgenes in mice. Proc. Natl. Acad. Sci. USA 88:478-482.
  28. Quintans, B., V. Alvarez-Iglesias, A. Salas, C. Phillips, M. V. Lareu, and A. Carracedo. 2004. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using snapshot minisequencing. Forensic Sci. Int. 140:251-257.
  29. Schall, T. J., M. Lewis, K. J. Koller, A. Lee, G. C. Rice, G. H. Wong, T. Gatanaga, G. A. Granger, R. Lentz, and H. Raab et al. 1990. Molecular cloning and expression of a receptor for human tumor necrosis factor. Cell 61:361-370.
  30. Stamenkovic, I., E. A. Clark, and B. Seed. 1989. A B-lymphocyte activation molecule related to the nerve growth factor receptor and induced by cytokines in carcinomas. EMBO J. 8:1403-1410.
  31. Taniguchi, M., T. Utsugi, K. Oyama, H. Mannen, M. Kobayashi, Y. Tanabe, A. Ogino, and S. Tsuji. 2004. Genotype of stearoyl-CoA desaturase is associated with fatty acid composition in Japanese Black cattle. Mamm. Genome 15:142-148.
  32. Trauth, B. C., C. Klas, A. M. Peters, S. Matzku, P. Moller, W. Falk, K. M. Debatin, and P. H. Krammer. 1989. Monoclonal antibody-mediated tumor regression by induction of apoptosis. Science 245:301-305.
  33. USDA. 1989. Official United States Standards for Grades of Beef Carcases. Agric. Marketing Serv.:USDA, Washington, DC, USA.
  34. Watanabe-Fukunaga, R., C. I. Brannan, N. Itoh, S. Yonehara, N. G. Copeland, N. A. Jenkins, and S. Nagata. 1992. The cDNA structure, expression, and chromosomal assignment of the mouse fas antigen. J. Immunol. 148:1274-1279.
  35. Wood, J. D., G. R. Nute, G. A. J. Fursey, and A. Cuthbertson. 1995. The effect of cooking conditions on the eating quality of pork. Meat Sci. 40:127-135.
  36. 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.
  37. Yonehara, S., A. Ishii, and M. Yonehara. 1989. A cell-killing monoclonal antibody (anti-Fas) to a cell surface antigen co-downregulated with the receptor of tumor necrosis factor. J. Exp. Med. 169:1747-1756.


Supported by : Rural Development Administration