DOI QR코드

DOI QR Code

Major SNP identification for oleic acid and marbling score which are associated with Korean cattle

한우의 올레인산과 근내지방도에 영향을 미치는 유전자 내 에스엔피 규명

  • Received : 2014.06.05
  • Accepted : 2014.08.04
  • Published : 2014.09.30

Abstract

This study is to identify the relationship between unsaturated fatty acids, which are indicators of beef flavor, and unsaturated fatty acid biosynthetic enzymes, which are associated with SNPs in the SCD, SREBPs, $PPAR{\gamma}$, FABP4, FASN and LPL in Hanwoo population. For analysis of fatty acid in Hanwoo, we used to Hanwoo steer(n=513). Also, following an analysis of the relationship raised from Gyeongbuk province region. FABP4; g.3977-325 T>C was selected and the distribution of beef grade of g.3977-325 T>C related in field trial was proved very excellent.

동물 유전학에 있어 한우의 우수한 품질개발과 통계학의 역할을 살펴본다. 본 연구는 한우에서 25 30개월에 특이적으로 유전자 발현이 일어나, 쇠고기 맛에 영향을 미치는 불포화지방산 및 육질등급에 직접적인 연관이 있는 것으로 알려진 6개의 유전자 (SCD, SREBPs, $PPAR{\gamma}$, FABP4, FASN, LPL)내의 30개 에스엔피와 가계 정보가 정확하고 도체 기록이 되어있으며, 포화지방산 및 불포화 지방산과 다가불포화 지방산을 분석한 한우 개체 513두에 대하여 연관 분석을 실시하였다. 그 중 FABP4; g.3977-325 T>C 에스엔피가 우수한 결과를 나타내고 있었다. 특히 선정된 에스엔피의 F-값은 91.36 및 30.00으로 다른 29개의 에스인피들 보다 우수한 효과를 보여주고 있었으며, 현장 농가에 직접적으로 재 검정한 결과 1+등급 이상이 나올 확률이 70.10%로 우수한 마커임을 입증할 수 있었다.

Keywords

References

  1. Abe, T., Saburi, J., Hasebe, H., Nakagawa, T., Kawamura, T., Saito, K., Nade, T., Misumi, S., Okumura, T., Kuchida, K., Hayashi, T., Nakane, S., Mitsuhasi, T., Nirasawa, K., Sugimoto, Y. and Kobayashi, E. (2008). Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F2 population from a cross between Japanese Black and Limousin. Journal of Animal science, 86, 2821-2832. https://doi.org/10.2527/jas.2007-0676
  2. Barendse, W., Harrison, B. E., Bunch, R. J. and Thoma, M. B. (2008). Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle. BMC Genetics, 9, 41-48.
  3. Barrett, J. C., Fry, B., Maller, J. and Daly, M. J. (2005). Haploview : Anaylsis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265. https://doi.org/10.1093/bioinformatics/bth457
  4. Barton, L., Kott, T., Bures, D., Rehak, D., Zahradkova, R. and Kottova, B. (2009). 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 Science, 9, 309-330.
  5. Chung, K. Y., Lunt, D. K., Kawachi, H., Yano, H. and Smith, S. B. (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. Journal of Animal Science, 85, 380-387. https://doi.org/10.2527/jas.2006-087
  6. Craig, D. W. and Stephan, D. A. (2005). Applications of whole genome high-density SNP genotyping. Expert Review of Molecular Diagnostics, 5, 159-170. https://doi.org/10.1586/14737159.5.2.159
  7. de Bakker, P. I., Yelensky, R., Pe'er, I., Gabriel, S. B., Daly, M. J. and Altshuler, D. (2005). Efficiency and power in genetic association studies. Nature Genetics, 37, 1217-1223. https://doi.org/10.1038/ng1669
  8. Dinh, T. T. N., Blanton, J. R., Riley, D. G., Chase, C. C., Coleman, S. W., Phillips, W. A., Brooks, J. C., Miller, M. F. and Thompson, L. D. (2010). Intramuscular fat and fatty acid composition of longissimus muscle from divergent pure breeds of cattle. Journal of Animal science, 88, 756-766. https://doi.org/10.2527/jas.2009-1951
  9. Falconer, D. S. (1989). Introduction to quantitative genetics, 3rd ed. Longman Scientific & Technical, Harlow, United Kingdom.
  10. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Waed, R., Lander, E. S., Daly, M. J. and Altshuler, D. (2002). The structure of haplotype blocks in the human genome. Sciences, 296, 2225-2229. https://doi.org/10.1126/science.1069424
  11. Gotoda, T., Yamada, N., Kawamura, M., Kozaki, K., Mori, N., Ishibashi, S., Shimano, H., Takaku, F., Yazaki, Y. and Furuichi, Y. (1991). Heterogeneous mutations in the human lipoprotein lipase gene in patients with familial lipoprotein lipase deficiency. Journal of Clinical Investigation, 88, 1856-1864. https://doi.org/10.1172/JCI115507
  12. Hedrick, P. W. (1987). Gametic disequilibrium measures: Proceed with caution. Genetics, 117, 331-341.
  13. Hoashi, S., Ashida, N., Ohsaki, H., Utsugi, T., Sasazaki, S., Taniguchi, M., Oyama, K., Mukai, F. and Mannen, H. (2007). Genotype of bovine sterol regulatory element binding protein-1(SREBP-1) is associated with fatty acid composition in Japanese Black cattle. Mammalian Genome, 18, 880-886. https://doi.org/10.1007/s00335-007-9072-y
  14. Horton, J. D., Shah, N. A., Warrington, J. A., Anderson, N. N., Park, S. W., Brown, M. S. and Goldstein, J. L. (2003). Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proceedings of the National Academy of Sciences, 100, 12027-12032. https://doi.org/10.1073/pnas.1534923100
  15. Ibi, T., Hirooka, H., Kahi, A. K., Sasae Y. and Sasaki, Y. (2005). Genotype environment interaction effects on carcass traits in Japanese Black cattle. Journal of Animal Science, 83, 1503-1510. https://doi.org/10.2527/2005.8371503x
  16. Kim, S. W., Lee, J. H., Won, Y. S., Kim, N. S. and Kim, K. S. (2010). Effect of the fatty acid synthase gene for beef quantity traits in Hanwoo breeding stock. Journal of Animal Science, 52, 9-16.
  17. Korea Animal Genetics & Breeding Lab. (2003). Animal breeding studies, Sunjin-Munwha Publishing Co, Seoul, Korea.
  18. Lee, H., Lee, M. H. and Chung, M. S. (1994). Comparison of flavor characteristics and palatability of beef obtained from various breeds. Korean Journal for Food Science of Animal Resources, 26, 500-506.
  19. Lee, H., Lee, S. H., Cho, Y. M., Yoon, H. B., Jeon, B. K., Oh, S. J., Kwon, M. S. and Yoon, D. H. (2004). Association between the polymorphism on intron 5 of the lipoprotein lipase gene and carcass traits in Hanwoo (Korean cattle). Journal of Animal Science and Technology, 46, 947-956. https://doi.org/10.5187/JAST.2004.46.6.947
  20. Lee, J., Jin, M., Lee., Y., Ha, J., Yeo, J. and Oh, D. (2014). Gene-gene interaction of fatty acid synthase (FASN) using multifactor dimensionality reduction method in Korean cattle. Molecular Biology Reports, 41, 2021-2027. https://doi.org/10.1007/s11033-014-3050-8
  21. Lee, J., Lee, Y., Lee, J., Oh, D., Jeong, D. and Kim, J. (2013a). Identification of Single Nucleotide Polymorphisms (SNPs) of the Bovine Growth Hormone (bGH) Gene associated with growth and carcass traits in Hanwoo. Asian-Australasian Journal of Animal Sciences, 26, 1359-1364. https://doi.org/10.5713/ajas.2013.13248
  22. Lee, J., Lee, J., Yeo, Y., Kim, J. (2013b). A SNP harvester analysis to better detect SNPs of CCDC158 gene that are associated with carcass quality traits in Hanwoo. Asian-Australasian Journal of Animal Sciences, 26, 766-771. https://doi.org/10.5713/ajas.2012.12715
  23. Lee, Y., Oh, D., Lee, J., La, B. and Yeo, J. (2013c). Novel single nucleotide polymorphism of bovine SREBP1 gene IA asociation with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo). Molecular Biology Reports, 40, 247-254. https://doi.org/10.1007/s11033-012-2055-4
  24. Mannen, H. (2011). Identification and utilization of genes associated with beef qualities. Animal Science Journal, 82, 1-7. https://doi.org/10.1111/j.1740-0929.2010.00845.x
  25. Matsuhashi, T., Maruyama, S., Uemoto, Y., Kobayashi, N., Mannen, H., Abe, T., Sakaguchi, S. and Kobayashi, E. (2011). Effects of bovine fatty acid synthase, stearoyl-coenzyme A desaturase, sterol regulatory element-binding protein 1, and growth hormone gene polymorphisms on fatty acid composition and carcass traits in Japanese Black cattle. Journal of Animal Science, 89, 12-22. https://doi.org/10.2527/jas.2010-3121
  26. Melton, S. L., Amiri, M., Davis, G. W. and Backus, W. R. (1982). Flavor and chemical characteristics of ground beef from grass-, forage-, grain- and grain-finished steers. Journal of Animal Science, 55, 77-87. https://doi.org/10.2527/jas1982.55177x
  27. Michal, J. J., Zhang, Z. W., Gaskins, C. T., and Jiang, Z. (2006). The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crosses. Animal Genetics, 37, 400-402. https://doi.org/10.1111/j.1365-2052.2006.01464.x
  28. Monson, F., Sanudo, C. and Sierra, I. (2005). Influence of breed and ageing time on sensory meat quality and consumer acceptability in intensively reared beef. Meat Science, 71, 471-479. https://doi.org/10.1016/j.meatsci.2005.04.026
  29. Oh, D. Y. (2014). Identification of the SNP within candidate gene associated with fatty acid composition in Hanwoo, Ph.D. Thesis, Yeungnam University, Kyungbuk.
  30. Oh, D., Jin, M. H., Lee, Y. S., Ha, J. J., Kim, B. K., Yeo, J. S. and Lee, J. Y. (2013a). Identification of Stearoyl-CoA desaturase (SCD) gene interactions in Korean native cattle based on the multifactor -dimensionality reduction method. Asian-Australasian Journal of Animal Sciences, 26, 1218-1228. https://doi.org/10.5713/ajas.2013.13058
  31. Oh, D., La, B., Lee, Y., Bun, Y., Lee, J., Yeo, G. and Yeo, J. (2013b). Identification of novel single nucleotide polymorphisms (SNPs) of the lipoprotein lipase (LPL) gene associated with fatty acidcomposition in Korean cattle. Molecular Biology Reports, 40, 3155-3163. https://doi.org/10.1007/s11033-012-2389-y
  32. Ohsaki, H., Thnaka, A., Hoashi, S., Sasazaki, S., Oyama, K., Taniguchi, M., Mukai, F. and Mannen, H. (2009). Effect of SCD and SREBP genotypes on fatty acid composition in adipose tissue of Japanese Black cattle herds. Journal of Animal Science, 80, 225-232. https://doi.org/10.1111/j.1740-0929.2009.00638.x
  33. Perez-Enciso, M and Misztal, I. (2004). Qxpak: A versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics, 20, 2792-2798. https://doi.org/10.1093/bioinformatics/bth331
  34. Rosenson, R. S. (2007). Effects of peroxisome proliferator-activated receptors on lipoprotein metabolism and glucose control in type 2 diabetes mellitus. The American Journal of Cardiology, 199, 96-104.
  35. Scheet, P. and Stephens, M. (2006). A fast and flexible statistical model for large-scale population genotype data : Applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics, 78, 629-644. https://doi.org/10.1086/502802
  36. Snelling, W. M., Casas, E., Stone, R. T., Keele, J. W., Harhay, G. P., Bennett, G. L. and Smith, T. P. L. (2005). Linkage mapping bovine EST-based SNP. BMC Genomics, 6, 74-83. https://doi.org/10.1186/1471-2164-6-74
  37. Storey, J. (2003). The positive false discovery rate : A Bayesian interpretation and the q-value. The Annals of Statistics, 31, 2013-2035. https://doi.org/10.1214/aos/1074290335
  38. Taniguchi, M., Utsugi, T., Oyama, K., Mannen, H., Kobayashi, M., Tanabe, Y., Ogino, A. and Tsuji, S. (2004). Genotype of stearoyl-CoA desaturase is associated with fatty acid composition in Japanese black cattle. Mammalian Genome, 14, 142-148.
  39. Tsuji, S. (2008). Kobe beef as international brand. In Symposium of Gyeungbuk Hanwoo Cluster, Daegu, Korea.
  40. Vreeland, W. N., Meagher, R. J. and Barron, A. E. (2002). Multiplexed, highthroughput genotype by single base extension and endlabeled free solution electrophoresis. Analytical Chemistry, 74, 4328-4333. https://doi.org/10.1021/ac0258094
  41. Waldman, R. C., Suess, G. G., Lewis, R. W., Bray, R. W. and Brungardt, V. H. (1965). Certain fatty acids of bovine tissue and their association with carcass characteristics. Journal of Animal Science, 24, 869.
  42. Wang, N., Akey, J. M., Zhang, K., Chakraborty, R. and Jin, L. (2002). Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. American Journal of Human Genetics, 71, 1227-34. https://doi.org/10.1086/344398
  43. Yoshimura, T. and Namikawa, K. (1983). Influence of breed, sex and anatomical location on lipid and fatty acid composition of bovine subcutaneous fat. Japanese Journal of Zootechnical Science, 54, 97-100.
  44. Zhang, S., Knight, T. J., Reecy, J. M. and Beitz, D. C. (2008). DNA polymorphisms in bovine fatty acid synthase are associated with beef fatty acid composition. Animal Genetics, 39, 62-70. https://doi.org/10.1111/j.1365-2052.2007.01681.x

Cited by

  1. Effect of different rearing systems on cortisol level and fatty acid composition in M-Longissimus of Korean native steers vol.26, pp.3, 2015, https://doi.org/10.7465/jkdi.2015.26.3.669
  2. Proposal of statistical model adjusted environmental factor in genetic research for high quality Hanwoo production vol.26, pp.6, 2015, https://doi.org/10.7465/jkdi.2015.26.6.1397
  3. Validation of diacylglycerol O-acyltransferase1 gene effect on milk yield using Bayesian regression vol.26, pp.6, 2015, https://doi.org/10.7465/jkdi.2015.26.6.1249
  4. Physicochemical properties of crust derived from dry-aged Holstein and Hanwoo loin vol.62, pp.5, 2014, https://doi.org/10.5187/jast.2020.62.5.692