A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations

  • Lee, Y.-M. (School of Biotechnology, Yeungnam University) ;
  • Han, C.-M. (School of Electrical Engineering and Information, Yeungnam University) ;
  • Li, Yi (School of Biotechnology, Yeungnam University) ;
  • Lee, J.-J. (Department of Animal Science, Chungbuk National University) ;
  • Kim, L.H. (Department of Genetic Epidemiology, SNP Genetics) ;
  • Kim, J.-H. (Hanwoo Improvement Center of National Agricultural Cooperative Federation) ;
  • Kim, D.-I. (Hanwoo Improvement Center of National Agricultural Cooperative Federation) ;
  • Lee, S.-S. (Hanwoo Improvement Center of National Agricultural Cooperative Federation) ;
  • Park, B.-L. (Department of Genetic Epidemiology, SNP Genetics) ;
  • Shin, H.-D. (Department of Genetic Epidemiology, SNP Genetics) ;
  • Kim, K.-S. (Department of Animal Science, Chungbuk National University) ;
  • Kim, N.-S. (Department of Animal Science, Chungbuk National University) ;
  • Kim, Jong-Joo (School of Biotechnology, Yeungnam University)
  • Received : 2010.01.14
  • Accepted : 2010.02.15
  • Published : 2010.04.01


The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.


Single Nucleotide Polymorphism;Whole Genome Association;Carcass Traits;Hanwoo


Supported by : Agriculture and Forestry of the Ministry of Agriculture, Forestry and Fisheries


  1. 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
  2. Benjamini, Y. and Y. Hochberg. 1995. Controlling the false discovery rat: a practical and powerful approach to multiple testing. J. R. Stat. Sco. B. 57:289-300
  3. Casas, E., S., D. Shackelford, J. W. Keele, R. T. Stone, S. M. Kappes and M. Koohmaraie. 2000. Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. J. Anim. Sci. 78:560-569
  4. Casas, E., S. D. Shackelford, J. W. Keele, M. Koohmaraie, T. P. L. Smith and R. T. Stone. 2003. Detection of quantitative trait loci for growth and carcass composition in cattle. J. Anim. Sci. 81:2976-2983
  5. 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
  6. Churchill, G. A. and R. W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971
  7. Druet, T., S. Fritz, D. Biochard and J. J. Colleau. 2006. Estimation of genetic parameters for quantitative trait loci for dairy traits in the French Holstein population. J. Dairy Sci. 89:4070-4076
  8. Goddard, M. E., B. Hayes, H. McPartlan and A. J. Chamberlain. 2006. Can the same genetic markers be used in multiple breeds? 8th World Congress on Genetics Applied to Livestock Production. Belo Horizonte, Brazil, 8 pp. 14-22
  9. Li, C., J. Basarab, W. M. Snelling, B. Benkel, J. Kneeland, B. Murdoch, C. Hansen and S. S. Moore. 2004. Identification and fine mapping of quantitative trait loci for backfat on bovine chromosomes 2, 5, 6, 19, 21, and 23 in a commercial line of Bos taurus. J. Anim. Sci. 82:967-972
  10. Takasuga, A., T. Watanabe, Y. Mizoguchi, T. Hirano, N. Ihara, A. Takano, K. Yokouchi, A. Fujikawa, K. Chiba, N. Kobayashi, K. Tatsuda, T. Oe, M. Furukawa-Kuroiwa, A. Nishimura-Abe, T. Fujita, K. Inoue, K. Mizoshita, A. Ogino and Y. Sugimoto. 2007. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-bydescent mapping. Mamm. Genome 18:125-136
  11. Decker, J. E., J. C. Pires, G. C. Conant, S. D. McKay, M. P. Heaton, J. Vilkki, C. M. Seabury, A. R. Caetano, G. S. Johnson, R. A. Brenneman, O. Hanotte, L. S. Eggert, P. Wiener, J.-J. Kim, K. S. Kim, T. S. Sonstegard, C. van Tassell, H. L. Neibergs, K. Chen, A. Cooper, J. McEwan, R. Brauning, M. C. McClure, M. M. Rolf, J. Kim, R. D. Schnabel and J. F. Taylor. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 106:18644-18649
  12. Zimin, A. V., A. L. Delcher, L. Florea, D. R. Kelley, M. C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, C. P. van Tassell, T. S. Sonstegard, G. Marcais, M. Roberts, P. Subramanian, J. A. Yorke and S. L. Salzberg. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10:R42
  13. Van Tassell, C. P., T. P. L. Smith, L. K. Matukumalli, J. F. Taylor, R. D. Schnabel, C. T. Lawley, C. D. Haudenschild, S. S. Moore, W. C. Warren and T. S. Sonstegard. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5:247-252
  14. The Bovine Genome Sequencing and Analysis Consortium, C. G. Elsik, R. L. Tellam and K. C. Worley. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528
  15. Sherman, E. L., J. D. Nkrumah and S. S. Moore. 2010. Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J. Anim. Sci. 88:16-22
  16. Falconer, D. S. and T. F. C. Mackay. 1996. Introduction to quantitative genetics. 4rh ed. Pearson/Prentice Hall. London
  17. Eck, S. H., A. benet-Pages, K. Flisikowski, T. Meitinger, R. Fries and T. M. Strom. 2009. Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol. 10:R82
  18. Abecasis, G. R., S. S. Cherny, W. O. Cookson and L. R. Cardon. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30:97-101
  19. Devlin, B. and N. Risch. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311-322
  20. Neter, J., W. Wasserman and M. H. Kutner. 1990. Applied linear statistical models. 3rd ed. Irwin. Boston
  21. Matukumalli, L. K., R. D. Schnabel, C. T. Lawley, T. S. Sonstegard, T. P. L. Smith, S. S. Moore, J. F. Taylor and C. P. van Tassell. 2008. Characterization of the cattle HapMap population using the Illumina Bovine-50K chip. Proc. Plant and Animal Genome XVI. San Diego, CA
  22. Sellner, E. M., J. W. Kim, M. C. McClure, K. H. Taylor, R. D. Schnabel and J. F. Taylor. 2007. Board-invited review: Application of genomic information in livestock. J. Anim. Sci. 85:3148-3158
  23. Van Eenennaam, A. L., J. Li, R. M. Thallman, R. L. Quaas, M. E. Dikeman, C. A. Gill, D. E. Franke and M. G. Thomas. 2007. Validation of commercial DNA tests for quantitative beef quality traits. J. Anim. Sci. 85:891-900
  24. Hayes, B. J., P. J. Bowman, A. J. Chamberlain and M. E. Goddard. 2009. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 92:433-443
  25. Kim, J.-J., F. Farnir, J. Savell and J. F. Taylor. 2003. Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. J. Anim. Sci. 81:1933-1942

Cited by

  1. Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip vol.9, pp.2, 2011,
  2. Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix vol.113, pp.6, 2014,
  3. Forward LASSO analysis for high-order interactions in genome-wide association study vol.15, pp.4, 2014,
  4. A Whole Genome Association Study on Meat Palatability in Hanwoo vol.27, pp.9, 2014,
  5. Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle vol.9, pp.10, 2014,
  6. A novel genetic variant database for Korean native cattle (Hanwoo): HanwooGDB vol.37, pp.1, 2015,
  7. A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo vol.30, pp.1, 2016,