Characterization of QTL for Growth and Meat Quality in Combined Pig QTL Populations

  • Li, Y. (School of Biotechnology, Yeungnam University) ;
  • Choi, B.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science) ;
  • Lee, Y.M. (School of Biotechnology, Yeungnam University) ;
  • Alam, M. (School of Biotechnology, Yeungnam University) ;
  • Lee, J.H. (Gyeongbuk Livestock Research Institute) ;
  • Kim, K.S. (Department of Animal Science, Chungbuk National University) ;
  • Baek, K.H. (School of Biotechnology, Yeungnam University) ;
  • Kim, J.J. (School of Biotechnology, Yeungnam University)
  • Received : 2011.07.12
  • Accepted : 2011.08.19
  • Published : 2011.12.01


This study was conducted to detect quantitative trait loci (QTL) for thirteen growth and meat quality traits in pigs by combing QTL experimental populations. Two F2 reference populations that were sired by Korea native pig (KNP) and dammed by Landrace (LN) or Yorkshire (YK) were generated to construct linkage maps using 123 genetic markers (mostly microsatellites) and to perform QTL analysis on porcine chromosomes (SSCs) 1, 2, 3, 6, 7, 8, 9, 11, 13, 14, and 15. A set of line-cross models was applied to detect QTL, and a series of lack-of-fit tests between the models was used to characterize inheritance mode of QTL. A total of 23, 11 and 19 QTL were detected at 5% chromosome-wise level for the data sets of KNP${\times}$LN, KNP${\times}$YK cross and joint sets of the two cross populations, respectively. With the joint data, two Mendelian expressed QTL for live weight and cooking loss were detected on SSC3 and SSC15 at 1% chromosome-wise level, respectively. Another Mendelian expressed QTL was detected for CIE a on SSC7 at 5% genome-wise level. Our results suggest that QTL analysis by combining data from two QTL populations increase power for QTL detection, which could provide more accurate genetic information in subsequent marker-assisted selection.


QTL;Joint Data;Meat Quality;Korean Native Pig;Landrace;Yorkshire


  1. AOAC. 1990. Official methods of analysis. 15th Ed. Association of official analytical chemists. Washington, DC, USA.
  2. Cameron, N. D. 1994. The value of pig selection experiments. Proceedings of the 5th World Congress on Genetics Applied to Livestock Production 19:41-48.
  3. Choy, Y. H., G. J. Jeon, T. K. Kim, B. H. Choi and H. W. Chung. 2002a. Ear type and coat color on growth performances of crossbred pigs. Asian-Aust. J. Anim. Sci. 15:1178-1181.
  4. Choy, Y. H., G. J. Jeon, T. K. Kim, B. H. Choi, I. C. Cheong, H. K. Lee, K. S. Seo, S. D. Kim, Y. I. Park and H. W. Chung. 2002b. Genetic analyses of carcass characteristics in crossbred pigs between Landrace sows and Korean wild boars. Asian-Aust. J. Anim. Sci. 15:1080-1084.
  5. Churchill, G. A. and R. W Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
  6. De Koning, D. J., H. Bovenhuis and J. A. van Arendonk .2002. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genetics 161: 931-938.
  7. De Koning, D. J., B. Harlizius, A. P. Rattink, M. A. Groenen, E. W. Brascamp and J. A. van Arendonk. 2001. Detection and characterization of quantitative trait loci for meat quality traits in pigs. J. Anim. Sci. 79:2812-2819.
  8. De Koning, D. J., A. P. Rattink, B. Harlizius, J. A. van Arendonk, E. W. Brascamp and M. A. Groenen. 2000. Genome-wise scan for body composition in pigs reveals important role of imprinting. Proc. Natl. Acad. Sci. USA 97:7947-7950.
  9. Dekkers, J. C., J. J. Kim, M. Malek, H. Thomsen, H. Lee, H. H. Zhao and M. F. Rothschild. 2003. A genome scan to detect QTL affecting growth, composition, and meat quality trait in a $Berkshire{\times}Yorkshire$ cross. Pages 1-21 in Proc. 28th National Swine Improvement Federation, Des Moines, IA.
  10. Edwards, D. B., C. W. Ernst, N. E. Raney, M. E. Doumit, M. D. Hoge and R. O. Bates. 2008. Quantitative trait locus mapping in an F2 $Duroc{\times}Pietrain$ resource population: II. Carcass and meat quality traits. J. Anim. Sci. 86:254-266.
  11. Georges, M. 2007. Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals. Annu. Rev. Genomics Hum. Genet. 8:131-162.
  12. Green, P., K. Fallis and S. Crooks. 1994. Documentation for CRIMAP version 2.4, Washington University School of Medicine, St. Louis, MO.
  13. Guo, Y. M., G. J. Lee, A. L. Archibald and C. S. Haley. 2008. Quantitative trait loci for production traits in pigs: a combined analysis of two $Meishan{\times}Large$ White populations. Anim. Genet. 39:486-495.
  14. Haley, C. S., S. A. Knott and J. M. Elsen. 1994. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195-207.
  15. Jeon, J. T., E. W. Park, H. J. Jeon, T. H. Kim, K. T. Lee and I. C. Cheong. 2003. A large-insert porcine library with seven fold genome coverage: a tool for positional cloning of candidate genes for major quantitative traits. Mol. Cells 16:113-116.
  16. Keats, B. J., S. L. Sherman, N. E. Morton, E. B. Robson, K. H. Buetow, P. E. Cartwright, A. Chakravarti, U. Francke, P. P. Green and J. Ott. 1991. Guidelines for human linkage maps: an international system for human linkage maps (ISLM, 1990). Genomics 9:557-560.
  17. Kim, E. H., B. H. Choi, K. S. Kim, C. K. Lee, B. W. Cho, T. H. Kim and J. J. Kim. 2007. Detection of Mendelian and parent-of-origin quantitative trait loci in a cross between Korean native pig and Landrace. I. growth and body composition traits. Asian-Aust. J. Anim. Sci. 20:669-676.
  18. Kim, K. S., J. S. Yeo and J. W. Kim. 2002. Assessment of genetic diversity of Korean native pig (Sus scrofa) using AFLP markers. Genes Genet. Syst. 77:361-368.
  19. Kim, T. H., B. H. Choi, H. K. Lee, H. S. Park, H. Y. Lee, D. H. Yoon, J. W. Lee, G. J. Jeon, I. C. Cheong, S. J. Oh and J. Y. Han. 2005a. Identification of quantitative traits loci (QTL) affecting growth traits in pigs. Asian-Aust. J. Anim. Sci. 18:1524-1528.
  20. Kim, T. H., K. S. Kim, B. H. Choi, D. H. Yoon, G. W. Jang, K. T. Lee, H. Y. Chung, H. Y. Lee, H. S. Park and J. W. Lee. 2005b. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J. Anim. Sci. 83:2255-2263.
  21. Kim, J. J., M. F. Rothschild, J. Beever, S. -Zas Rodriguez and J. C. Dekkers. 2005c. Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J. Anim. Sci. 83:1229-1240.
  22. Kim, J. J., H. Zhao, H. Thomsen, M. F. Rothschild and J. C. Dekkers. 2005d. Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet. Res. 85:235-48.
  23. Kristensen, L. and P. P. Purslow. 2001. The effect of ageing on the water-holding capacity of pork: Role of cytoskeletal proteins. Meat Sci. 58:17-23.
  24. Lee, H. K., S. S. Lee, T. H. Kim, G. J. Jeon, H. W. Jung, Y. S. Shin, J. Y. Han, B. H. Choi and I. C. Cheong. 2003. Detection of imprinted quantitative trait loci (QTL) for growth traits in pigs. Asian-Aust. J. Anim. Sci. 16:1087-1092.
  25. Liu, G., J. J. Kim, E. Jonas, K. Wimmers, S. Ponsuksili, E. Murani, C. Phatsara, E. Tholen, H. Juengst, D. Tesfaye, J. L. Chen and K. Schellander. 2008. Combined line-cross and half-sib QTL analysis in Duroc-Pietrain population. Mamm. Genome. 19:429-438.
  26. Moon, J. K., K. S. Kim, J. J. Kim, B. H. Choi, B. W. Cho, T. H. Kim and C. K. Lee. 2009. Differentially expressed transcripts in adipose tissue between Korean native pig and Yorkshire breeds. Anim. Genet. 40:115-118.
  27. Ovilo, C., A. Clop, J. L. Noguera, M. A. Oliver, C. Barragan, C. Rodriguez, L. Silio, M. A. Toro, A. Coll, J. M. Folch, A. Sanchez, D. Babot, L. Varona and M. Perez-Enciso. 2002. Quantitative trait locus mapping for meat quality traits in an $Iberian{\times}Landrace$ F2 pig population. J. Anim. Sci. 80:2801-2808.
  28. Rohrer, G. A., R. M. Thallman, S. Shackelford, T. Wheeler and M. Koohmaraie. 2006. A genome scan for loci affecting pork quality in a Duroc-Landrace F population. Anim. Genet. 37:17-27.
  29. Rothschild, M. F., Z. L. Hu and Z. Jiang. 2007. Advances in QTL mapping in pigs. Int. J. Biol. Sci. 3:192-197.
  30. Thomsen, H., H. K. Lee, M. F. Rothschild, M. Malek and J. C. Dekkers. 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. J. Anim. Sci. 82:2213-2228.
  31. Wheeler, T. L., S. D. Shackelford and M. Koohmaraie. 2000. Variation in proteolysis, sarcomere length, collagen content, and tenderness among major pork muscles. J. Anim. Sci. 78:958-965.

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