- Volume 26 Issue 9
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Identification of Stearoyl-CoA Desaturase (SCD) Gene Interactions in Korean Native Cattle Based on the Multifactor-dimensionality Reduction Method
- Oh, Dong-Yep (Livestock Research institute) ;
- Jin, Me-Hyun (Department of Statistics, Yeungnam University) ;
- Lee, Yoon-Seok (Institute of Green Bio Science and Technology, Seoul National University) ;
- Ha, Jae-Jung (Livestock Research institute) ;
- Kim, Byung-Ki (Livestock Research institute) ;
- Yeo, Jung-Sou (School of Biotechnology, Yeungnam University) ;
- Lee, Jea-Young (Department of Statistics, Yeungnam University)
- Received : 2013.01.22
- Accepted : 2013.05.26
- Published : 2013.09.01
Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase1 (SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.
Supported by : Yeungnam University
- Kwon, E. G., B. K. Park, H. C. Kim, Y. M. Cho, T. Il Kim, and S. S. Chang. 2009. Effects of fattening period on growth performance, carcass characteristics and lipogenic gene expression in Hanwoo steers. Asian-Aust. J. Anim. Sci. 22: 1654-1660. https://doi.org/10.5713/ajas.2009.90257
- Lee, S. H., D. H. Yoon, N. J. Choi, S. H. Hwang, E. Y. Cheong, S. J. Oh, Il. C. Cheong, and C. S. Lee. 2005. Developmental relationship of unsaturated fatty acid composition and stearoyl-CoA desaturase mRNA level in Hanwoo steers' muscle. Asian-Aust. J. Anim. Sci. 18:562-566. https://doi.org/10.5713/ajas.2005.562
- Lengi, A. J., and B. A. Corl. 2007. Identification and characterization of a novel bovine stearoyl-CoA desaturase isoform with homology to human SCD5. Lipids 42:499-508. https://doi.org/10.1007/s11745-007-3056-2
- Mandell, I. B., J. G. Buchanan-Smith, and C. P. Campbell. 1998. Effects of forage vs grain feeding on carcass characteristics, fatty acid composition, and beef quality in Limousin-cross steers when time on feed is controlled. J. Anim. Sci. 76:2619-2630.
- Matsumoto, N., F. Kakihara, S. Kimura, Y. Kurebayashi, M. Hirai, M. Yohda, and S. Hasegawa. 2007. Single nucleotide polymorphism genotyping of CYP2C19 using a new automated system. Anal. Biochem. 370:121-123. https://doi.org/10.1016/j.ab.2007.06.006
- Melton, S. L., M. Amiri, G. W. Davis, and W. R. Backus. 1982. Flavor and chemical characteristics of ground beef from grass-, forage-, grain- and grain-finished steers. J. Anim. Sci. 55:77-87.
- Milanesi, E., L. Nicoloso, and P. Crepaldi. 2008. Stearoyl-CoA desaturase (SCD) gene polymorphism in Italian cattle breeds. J. Anim. Breed. Genet. 125:63-67. https://doi.org/10.1111/j.1439-0388.2007.00697.x
- Miyazaki, M., A. Dobrzyn, W. C. Man, K. Chu, H. Sampath, D. B. Westerling, and H. B. Hedrick. 1979. Fatty acid composition of bovine lipids as influenced by diet, sex and anatomical location and relationship to sensory characteristics. J. Anim. Sci. 48:1343-1348.
- Oh, D. Y., Y. S. Lee, and J. S. Yeo. 2011. Identification of the SNP (single nucleotide polymorphism) of the stearoyl-CoA desaturase (SCD) associated with unsaturated fatty acid in Hanwoo. Asian-Aust. J. Anim. Sci. 24:757-765. https://doi.org/10.5713/ajas.2011.10410
- Oh, D. Y., Y. S. Lee, B. M. La, and J. S. Yeo. 2012. Identification of the SNP (single nucleotide polymorphism) for fatty acid composition associated with beef flavor-related FABP4 (fatty acid binding protein 4) in Korean cattle. Asian-Aust. J. Anim. Sci. 25:913-920. https://doi.org/10.5713/ajas.2012.12078
- Ohsaki, H., A. Thnaka, S. Hoashi, S. Sasazaki, K. Oyama, M. Taniguchi, F. Mukai, and H. Mannen. 2009. Effect of SCD and SREBP genotypes on fatty acid composition in adipose tissue of Japanese Black cattle herds. Anim. Sci. J. 80:225-232. https://doi.org/10.1111/j.1740-0929.2009.00638.x
- O'eefe, P. W., G. H. Wellington, L. R. Mattick, and J. R. Stouffer. 1968. Composition of bovine muscle lipids at various carcass locations. J. Food. Sci. 33:188-192. https://doi.org/10.1111/j.1365-2621.1968.tb01347.x
- Paolo, G. 2003. Applied data mining: Statistical methods for business and industry (Statistics in practice. John Wiley & Sons, England
- Paton, C. M., and J. M. Ntambi. 2009. Biochemical and physiological function of stearoyl-CoA desaturase. Am. J. Physiol. Endocrinol. Metab. 297:E28-E37. https://doi.org/10.1152/ajpendo.90897.2008
- Barton, L., T. Kott, D. Bures, D. Rehak, R. Zahradkova, and B. Kottova. 2010. The polymorphism of stearoyl-CoA desaturase (SCD1) and sterol regulatory element binding proyein-1 (SREBP-1) genes and their association with the fatty acid profile of muscle and subcutaneous fat in Fleckvieh bulls. Meat Sci. 85(1):15-20.
- Bastione, L., M. Reilly, D. J. Rader, and A. S. Foulkes. 2004. MDR and PRP: A comparison of methods for high-order genotype-phenotype associations. Hum. Hered. 58:82-92. https://doi.org/10.1159/000083029
- Chung, K. Y., D. K. Lunt, H. Kawachi, H. Yano, and S. B. Smith. 2007. Lipogenesis and stearoyl-CoA desaturase gene expression and enzyme activity in adipose tissue of short- and long-fed Angus and Wagyu steers fed corn- or hay-based diets. J. Anim. Sci. 85:380-387. https://doi.org/10.2527/jas.2006-087
- Chung, Y. J., S. Y. Lee, and T. S. Park. 2006. Multifactor dimensionality reduction in the presence of missing observations. In: Proceedings of the 2006 Spring Korean Statistical Society Conference, Pusan National University, Pusan. pp. 31-36.
- Erkkila, A., V. D. F. de Mello, U. Riserius, and D. E. Laaksonen. 2008. Dietary fatty acid and cardiovascular disease: An epidemiological approach. Prog. Lipid Res. 47:172-187. https://doi.org/10.1016/j.plipres.2008.01.004
- Folch, J., M. Lee, and G. H. Sloane Stanley. 1957. A simple method for the isolation and purification of total lipids from animal tissue. J. Biol. Chem. 226:497-509.
- Good, P. 1994. Permutation test, a practical guide to resampling for testing hypotheses. Springer, New York.
- Hahn, L. W., M. D. Ritchie, and J. H. Moore. 2003. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19:376-382. https://doi.org/10.1093/bioinformatics/btf869
- Inoue, K., N. Shoji, and M. Kobayashi. 2008. Genetic relations among fat melting point, fatty acid composition and carcass traits in Japanese Black cattle. Anim. Sci. J. 79:1-8.
- Kgwatalala, P. M., E. M. Ibeagha-Awemu, J. F. Hayes, and X. Zhao. 2007. Single nucleotide polymorphism in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows. Mitochondrial DNA. 18:357-362.
- Kuchel, H., B. D. Siebert, C. D. K. Bottema, G. C. Webb, A. M. Crawford, S. J. Duncan, P. A. McDonald, J. C. McEwan, and W. S. Pitchford. 2004. Physical mapping of the stearoyl-CoA desaturase (SCD) locus in sheep. Anim. Genet. 35:163. https://doi.org/10.1111/j.1365-2052.2004.01114.x
- Alexander, L. J., M. D. MacNeil, T. W. Geary, W. M. Snelling, D. C. Rule, and J. A. Scanga. 2007. Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Anim. Genet. 38: 506-513. https://doi.org/10.1111/j.1365-2052.2007.01643.x
- Barendse, W., A. Reverter, R. J. Bunch, B. E. Harrison, W. Barris, and M. B. Thomas. 2007. A validated whole-genome association study of efficient food conversion in cattle. Genetics 176:1893-1905. https://doi.org/10.1534/genetics.107.072637
- Ritchie, M. D., L. W. Hahn, N. Roodi, L. R. Bailey, W. D. Dupont, F. F. Parl, and J. H. Moore. 2001. Multifactor-dimensionality reduction reveals high-order interactions among estrogen- metabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69:138-147. https://doi.org/10.1086/321276
- Scollan, N., J. F. Hocquette, K. Nuernberg, D. Dannenberger, and I. M. A. Richardson. 2006. Innovation in beef production system that enhance the nutritional and health value of beef lipids and their relationship with meat quality. Meat Sci. 74:17-33. https://doi.org/10.1016/j.meatsci.2006.05.002
- Shin, S. C. 2006. The development of DNA markers related to carcass and meat quality traits in Korean cattle. MS thesis, Sang Ji University.
- Smith, S. B., D. K. Lunt, K. Y. Chung, C. B. Choi, R. K. Tume, and M. Zembayashi. 2006. Adiposity, fatty acid composition, and delta-9 desaturase activity during growth in beef cattle. J. Anim. Sci. 77:478-486. https://doi.org/10.1111/j.1740-0929.2006.00375.x
- Taniguchi, M., H. Mannen, K. Oyama, Y. Shimakura, A. Oka, H. Watanabe, T. Kojima, M. Komatsu, G. S. Harper, and S. Tsuji. 2004. Differences in stearoyl-CoA desaturase mRNA levels between Japanese Black and Holstein cattle. Livest. Prod. Sci. 87:215-220. https://doi.org/10.1016/j.livprodsci.2003.07.008
- 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. 14:142-148.
- Tsuji, S., K. Itoh, S. Sasazaki, H. Mannen, K. Oyama, M. Shojo, and F. Mulai. 2004. An association study using AFLP markers and application to a beef cattle breeding population. Anim. Genent. 35:40-43. https://doi.org/10.1111/j.1365-2052.2003.01084.x
- Tsuji, S. 2008. Kobe beef as international brand. Symposium of Gyeungbuk Hanwoo Cluster.
- Vreeland, W. N., R. J. Meagher, and A. E. Barron. 2002. Multiplexed, highthroughput genotype by single base extension and endlabeled free solution electrophoresis. Anal. Chem. 74:4328-4333. https://doi.org/10.1021/ac0258094
- Webb, E. C., and H. A. O'eil. 2008. The animal fat paradox and meat quality. Meat Sci. 80:28-36. https://doi.org/10.1016/j.meatsci.2008.05.029
- Zhang, S., T. J. Knight, J. M. Reecy, and D. C. Beitz. 2008. DNA polymorphisms in bovine fatty acid synthase are associated with beef fatty acid composition. Anim. Genet. 39:62-70. https://doi.org/10.1111/j.1365-2052.2007.01681.x
- Major SNP identification for oleic acid and marbling score which are associated with Korean cattle vol.25, pp.5, 2014, https://doi.org/10.7465/jkdi.2014.25.5.1011
- Population structure and genomic inbreeding in nine Swiss dairy cattle populations vol.49, pp.1, 2017, https://doi.org/10.1186/s12711-017-0358-6
- , and Oral Cancer Risk vol.19, pp.4, 2015, https://doi.org/10.1089/omi.2014.0121
- Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle vol.40, pp.9, 2018, https://doi.org/10.1007/s13258-018-0704-2