Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed

  • Lee, Taeheon (Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Shin, Dong-Hyun (Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Cho, Seoae (C&K genomics, Seoul National University Research Park) ;
  • Kang, Hyun Sung (Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University) ;
  • Kim, Sung Hoon (Genomic Informatics Center, Hankyong National University) ;
  • Lee, Hak-Kyo (Genomic Informatics Center, Hankyong National University) ;
  • Kim, Heebal (Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Seo, Kang-Seok (Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University)
  • Received : 2013.07.04
  • Accepted : 2013.09.07
  • Published : 2014.03.01


The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.


  1. Barrett, J., B. Fry, J. Maller, and M. Daly. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
  2. Andersson, L. 2001. Genetic dissection of phenotypic diversity in farm animals. Nat. Rev. Genet. 2:130-138.
  3. Andersson, L. and M. Georges. 2004. Domestic-animal genomics: deciphering the genetics of complex traits. Nat. Rev. Genet. 5:202-212.
  4. Aulchenko, Y. S., D. J. de Koning, and C. Haley. 2007. Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177:577-585.
  5. Davoli, R. and Braglia, S. 2007. Molecular approaches in pig breeding to improve meat quality. Brief. Funct. Genomic. Proteomic. 6:313-321.
  6. De Vries, A., L. Faucitano, A. Sosnicki, and G. Plastow. 2000. The use of gene technology for optimal development of pork meat quality. Food. Chem. 69:397-405.
  7. Duggal, P., E. M. Gillanders, T. N. Holmes, and J. E. Bailey-Wilson. 2008. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics 9:516.
  8. Fonseca, S., I. Wilson, G. Horgan, and C. Maltin. 2003. Slow fiber cluster pattern in pig longissimus thoracis muscle: implications for myogenesis. J. Anim. Sci. 81:973-983.
  9. Gilmour, A., B. Gogel, B. Cullis, R. Thompson, D. Butler, M. Cherry, D. Collins, G. Dutkowski, S. Harding, and K. Haskard. 2009. ASReml user guide release 3.0. VSN International Ltd., UK. 275.
  10. Friendly, M. 2002. Corrgrams. Am. Stat. 56:316-324.
  11. Gabriel, S. B., S. F. Schaffner, H. Nguyen, J. M. Moore, J. Roy, B. Blumenstiel, J. Higgins, M. DeFelice, A. Lochner, and M. Faggart. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
  12. Gao, J., H. Lin, Z. Song, and H. Jiao. 2008. Corticosterone alters meat quality by changing pre-and postslaughter muscle metabolism. Poult. Sci. 87:1609-1617.
  13. Goodwin, R. and S. Burroughs. 1995. Genetic evaluation terminal line program results. National Pork Producers Council, Des Moines, IA.
  14. Hu, Z.-L., C. A. Park, X.-L. Wu, and J. M. Reecy. 2013. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucl. Acids Res. 41:D871-D879.
  15. Imamura, M., S. Maeda, T. Yamauchi, K. Hara, K. Yasuda, T. Morizono, A. Takahashi, M. Horikoshi, M. Nakamura, and H. Fujita. 2012. A single-nucleotide polymorphism in ANK1 is associated with susceptibility to type 2 diabetes in Japanese populations. Hum. Mol. Genet. 21:3042-3049.
  16. Karasik, D., C. L. Cheung, Y. Zhou, L. A. Cupples, D. P. Kiel, and S. Demissie. 2012. Genome-wide association of an integrated osteoporosis-related phenotype: Is there evidence for pleiotropic genes? J. Bone Miner. Res. 27:319-330.
  17. Kent, W. J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
  18. Rosenvold, K. and H. J. Andersen. 2003. Factors of significance for pork quality-a review. Meat Sci. 64:219-237.
  19. Luo, W., D. Cheng, S. Chen, L. Wang, Y. Li, X. Ma, X. Song, X. Liu, W. Li, and J. Liang. 2012. Genome-wide association analysis of meat quality traits in a porcine Large White${\times}$Minzhu intercross population. Int. J. Biol. Sci. 8:580-595.
  20. Ma, J., J. Yang, L. Zhou, Z. Zhang, H. Ma, X. Xie, F. Zhang, X. Xiong, L. Cui, and H. Yang. 2013. Genome-wide association study of meat quality traits in a White Duroc${\times}$Erhualian F2 intercross and Chinese Sutai pigs. PloS one 8:e64047.
  21. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. De Bakker, and M. J. Daly. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81:559-575.
  22. Tabassum, R., S. Chavali, O. P. Dwivedi, N. Tandon, and D. Bharadwaj. 2008. Genetic variants of FOXA2: risk of type 2 diabetes and effect on metabolic traits in North Indians. J. Hum. Genet. 53:957-965.
  23. Tsai, L.-C. L. and J. A. Beavo. 2011. The roles of cyclic nucleotide phosphodiesterases (PDEs) in steroidogenesis. Curr. Opin. Pharmacol. 11:670-675.
  24. Tsai, L.-C. L., M. Shimizu-Albergine, and J. A. Beavo. 2011. The high-affinity cAMP-specific phosphodiesterase 8B controls steroidogenesis in the mouse adrenal gland. Mol. Pharmacol. 79:639-648.
  25. Wimmers, K., E. Murani, M. Te Pas, K. Chang, R. Davoli, J. Merks, H. Henne, M. Muraniova, N. Da Costa, and B. Harlizius. 2007. Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition. Anim. Genet. 38:474-484.
  26. Wolfrum, C., E. Asilmaz, E. Luca, J. M. Friedman, and M. Stoffel. 2004. Foxa2 regulates lipid metabolism and ketogenesis in the liver during fasting and in diabetes. Nature 432:1027-1032.
  27. Xu, T., W. Huang, X. Zhang, B. Ye, H. Zhou, and S. Hou. 2012. Identification and characterization of genes related to the development of breast muscles in Pekin duck. Mol. Biol. Rep. 39:7647-7655.
  28. Yang, J., W. N. Weedon, S. Purcell, G. Lettre, K. Estrada, C. J. Willer, A. V. Smith, E. Ingelsson, J. R. O'Connell, and M. Mangino. 2011. Genomic inflation factors under polygenic inheritance. Eur. J. Hum. Genet. 19:807-812.

Cited by

  1. Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds vol.13, pp.4, 2015,
  2. Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits vol.28, pp.11, 2015,
  3. Investigations on Genetic Architecture of Hairy Loci in Dairy Cattle by Using Single and Whole Genome Regression Approaches vol.29, pp.7, 2015,
  4. Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection vol.4, pp.4, 2015,
  5. Detection of SNPs in the BMP6 Gene and Their Association with Carcass and Bone Traits in Chicken vol.19, pp.4, 2017,
  6. Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine vol.31, pp.12, 2018,
  7. Multivariate genome-wide association studies on tenderness of Berkshire and Duroc pig breeds vol.40, pp.7, 2018,
  8. Relationship between VRTN gene polymorphism and growth, slaughter and meat quality traits in three polish pig breeds vol.42, pp.5, 2018,