Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Body Conformation Traits in a Hanwoo Population

  • Alama, M. (School of Biotechnology, Yeungnam University) ;
  • Lee, Y.M. (School of Biotechnology, Yeungnam University) ;
  • Park, B.L. (Department of Genetic Epidemiology, SNPGenetics) ;
  • Kim, J.H. (Hanwoo Improvement Center of National Agricultural Cooperative Federation) ;
  • Lee, S.S. (Hanwoo Improvement Center of National Agricultural Cooperative Federation) ;
  • Shin, H.D. (Department of Genetic Epidemiology, SNPGenetics) ;
  • Kim, K.S. (Department of Animal Science, Chungbuk National University) ;
  • Kim, N.S. (Department of Animal Science, Chungbuk National University) ;
  • Kim, J.J. (School of Biotechnology, Yeungnam University)
  • Received : 2011.01.17
  • Accepted : 2011.02.19
  • Published : 2011.03.01


A whole genome association (WGA) study was conducted to identify quantitative trait loci (QTL) for body conformation traits in Hanwoo cattle. The phenotypes of 497 steers were recorded from the Hanwoo Improvement Center of National Agricultural Cooperative Federation, Seosan, Korea, and analyzed using the Illumina Bovine 50 k SNP chip. A set of 35,987 SNPs that were available in the Hanwoo population was selected from the chip. After adjustments for the effects of year-season of birth, region and sire, phenotypes were regressed on each SNP using a linear regression model. Three hundred nineteen SNPs were detected for the ten conformation traits (p<0.003). For the significant SNPs, stepwise regression procedures were applied to determine best sets of markers. A total of 72 SNPs were selected (p<0.001), for which the sets of 5, 9, 10, 9, 8, 11, 4, 6, 3 and 7 SNPs were determined for height at withers, rump height, body length, chest depth, chest width, rump length, hip width, thurl width, pinbone width and heart girth, respectively. About 7-26% of the total phenotypic variation was explained by the set of SNPs for each trait. QTL for the conformation traits were harbored on most bovine chromosomes (BTAs). Four SNPs with pleiotropic effects on height at withers and rump height were detected on BTAs 3, 4, 6 and 16. A SNP with pleiotropic effects on chest width and rump length was also detected on BTA10. Two QTL regions, i.e. between 87 and 97 Mb in BTA3 and between 41 and 44 Mb in BTA7, were found, in which SNPs were detected for the five and three conformation traits, respectively. The detected SNPs need to be validated in other Hanwoo populations for commercial application to the genetic improvement of conformation characteristics in Hanwoo via marker-assisted selection (MAS).


  1. Abe, T., J. Saburi, H. Hasebe, T. Nakagawa, T. Kawamura, K. Saito, T. Nade, S. Misumi, T. Okumura, K. Kuchida, T. Hayashi, S. Nakane, T. Mitsuhashi, K. Nirasawa, Y. Sugimoto and E. Kobayashi. 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. J. Anim. Sci. 86:2821-2832.
  2. Ashwell, M. S., D. W. Heyen, J. I. Weller, M. Ron, T. S. Sonstegard, C. P. Van Tassell and H. A. Lewin. 2005. Detection of quantitative trait loci influencing conformation traits and calving ease in Holstein-Friesian cattle. J. Dairy Sci. 88:4111-4119.
  3. Ashwell, M. S., Y. Da, P. M. Vanraden, C. E. Rexroad, Jr. and R. H. Miller. 1998. Detection of putative loci affecting conformational type traits in elite population of United States Holsteins using microsatellite markers. J. Dairy Sci. 81:1120-1125.
  4. Benjamini, Y. and Y. Hochberg. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B. Stat. Methodol. 57:289-300.
  5. Biochrad, D., C. Grohs, F. Bourgeois, F. Cerqueira, R. Faugeras, A. Neau, R. Rupp, Y. Amigues, M. Y. Boscher and H. Leveziel. 2003. Detection of genes influencing economic traits in three French dairy cattle breeds. Genet. Sel. Evol. 35:77-101.
  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. Casas, E., S. D. Shackelford, J. W. Keele, M. Koohmaraie, T. P. Smith and R. T. Stone. 2003. Detection of quantitative trait loci for growth and carcass composition in cattle. J. Anim. Sci. 81:2976-2983.
  8. 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.
  9. Churchill, G. A. and R. W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
  10. 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.
  11. Falconer, D. S. and T. F. C. Mackay. 1996. Introduction to quantitative genetics. 4rh ed. Pearson/Prentice Hall. London.
  12. Gibbs, R. A., J. F. Taylor, C. P. Van Tassell, W. Barendse, K. A. Eversole, C. A. Gill, R. D. Green, D. L. Hamernik, S. M. Kappes, S. Lien, L. K. Matukumalli, J. C. McEwan, L. V. Nazareth, R. D. Schnabel, G. M. Weinstock, D. A. Wheeler, P. Ajmone-Marsan, P. J. Boettcher, A. R. Caetano, J. F. Garcia, O. Hanotte, P. Mariani, L. C. Skow, T. S. Sonstegard, J. L. Williams, B. Diallo, L. Hailemariam, M. L. Martinez, C. A. Morris and L. O. Silva, et al. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-532.
  13. Hiendleder, S., H. Thomsen, N. Reinsch, J. Bennewitz, B. Leyhe-Horn, C. Looft, N. Xu, I. Medjugorac, I. Russ, C. Kuhn, G. A. Brockmann, J. Blumel, B. Brenig, F. Reinhardt, R. Reents, G. Averdunk, M. Schwerin, M. Forster, E. Kalm and G. Erhardt. 2003. Mapping of QTL for body conformation and behavior in cattle. J. Hered. 94:496-506.
  14. Keele, J. W., S. D. Shackelford, S. M. Kappes, M. Koohmaraie and R. T. Stone. 1999. A region on bovine chromosome 15 influences beef longissimus tenderness in steers. J. Anim. Sci. 77:1364-1371.
  15. 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.
  16. Kolbehdari, D., Z. Wang, J. R. Grant, B. Murdoch, A. Prasad, Z. Xiu, E. Marques, P. Stothard and S. S. Moore. 2008. A wholegenome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls. J. Dairy Sci. 91:2844-2856.
  17. Lee, Y.-M., C.-M. Han, Y. Li, J.-J. Lee, L.-H. Kim, J.-H. Kim, D.-I. Kim, S.-S. Lee, B.-L. Park, H.-D. Shin, K.-S. Kim, N.-S. Kim and J.-J. Kim. 2010. A whole genome association study to detect single nucleotide polymorphism for carcass traits in Hanwoo populations. Asian-Aust. J. Anim. Sci. 23(4):417-424.
  18. Malau-Aduli, A. E. O., T. Niibayashi, T. Kojima, K. Oshima, Y. Mizoguchi and M. Komatsu. 2005. Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle. Anim. Sci. J. 76:19-27.
  19. Malau-Aduli, A. E. O., T. Niibayashi, T. Kojima, K. Oshima, Y. Mizoguchi and M. Komatsu. 2007. Detection and mapping of QTL on bovine chromosomes 2 and 5 segregating for live weight, average daily gain and body measurements in Japanese black cattle. J. Cell Anim. Biol. 1(3):34-43.
  20. 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.
  21. Neter, J., W. Wasserman and M. H. Kutner. 1990. Applied linear statistical models. 3rd ed. Irwin. Boston.
  22. Schnabel, R. D., T. S. Sonstegard, J. F. Taylor and M. S. Ashwell. 2005. Whole-genome scan to detect QTL for milk production, conformation, fertility and functional traits in two US Holstein families. Anim. Genet. 36:408-416.
  23. Schrooten, C., H. Bovenhuis, W. Coppieters and J. A. M. Van Arendonk. 2000. Whole genome scan to detect quantitative trait loci for conformation and functional traits in dairy cattle. J. Dairy Sci. 83:795-806.
  24. Seaton, G., C. S. Haley, S. A. Knott, M. Kearsey and P. M. Visscher. 2002. QTL express: Mapping quantitative trait loci in simple and complex pedigree. Bioinformatics 18:339-340.
  25. 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.
  26. 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.
  27. Sladek, R., G. Rocheleau and J. Rung. 2007. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445 (7130):881-885.
  28. Stone, R. T., J. W. Keele, S. D. Shackelford, S. M. Kappes and M. Koohmaraie. 1999. A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits. J. Anim. Sci. 77:1379-1384.
  29. 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.
  30. 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.
  31. 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.
  32. Varade, P. and S. Z. Ali. 2001. Body measurements on nondescript bullocks of Buldhana district in Maharashtra. J. Appl. Zool. Res. 12:71-72.
  33. Visscher, P. M. and M. E. Goddard. 1995. Genetic parameters for milk yield, survival, workability, and type traits for Australian dairy cattle. J. Dairy Sci. 78:205-220.
  34. 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.

Cited by

  1. Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip vol.9, pp.2, 2011,
  2. A Whole Genome Association Study on Meat Palatability in Hanwoo vol.27, pp.9, 2014,
  3. Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep vol.37, pp.2, 2014,
  4. Genome Association Study for Visual Scores in Nellore Cattle Measured at Weaning vol.20, pp.1, 2019,