DOI QR코드

DOI QR Code

Investigation of Single Nucleotide Polymorphisms in Porcine Chromosome 2 Quantitative Trait Loci for Meat Quality Traits

  • Do, K.T. (Department of Animal Science, Chungbuk National University) ;
  • Ha, Y. (Department of Animal Science, Chungbuk National University) ;
  • Mote, B.E. (Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University) ;
  • Rothschild, M.F. (Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University) ;
  • Choi, B.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Lee, S.S. (Animal Genetic Resouce Station, National Institute of Animal Science, RDA) ;
  • Kim, T.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Cho, B.W. (College of Natural Resource and Life Sciences, Pusan National Univeristy) ;
  • Kim, K.S. (Department of Animal Science, Chungbuk National University)
  • Received : 2007.03.05
  • Accepted : 2007.07.23
  • Published : 2008.02.01

Abstract

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

Keywords

Pig;Quantitative Trait Loci;Pig Chromosome 2;Single Nucleotide Polymorphism;Meat Quality

Acknowledgement

Supported by : Korea Rural Administration

References

  1. 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. .2005. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J. Anim. Sci. 83(10):2255-2263. https://doi.org/10.2527/2005.83102255x
  2. Larzul, C., L. Lefaucheur, P. Ecolan, J. Gogue, A. Talamnt, P. Sellier, P. Le Roy and G. Monin. 1997. Phenotypic and genetic parameters for Longissimus muscle fiber characteristics in relation to growth, carcass, and meat quality traits in Large White pigs. J. Anim. Sci. 75:3126-3137. https://doi.org/10.2527/1997.75123126x
  3. Le Roy, P., J. Naveau, J. M. Elsen and P. Sellier. 1990. Evidence for a new major gene influencing meat quality in pigs. Genet. Res. 55(1):33-40. https://doi.org/10.1017/S0016672300025179
  4. Malek, M., J. C. Dekkers, H. K. Lee, T. J. Baas, K. Prusa, E. Huff-Lonergan and M. F. Rothschild. 2001. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mamm. Genome. 12(8):637-645. https://doi.org/10.1007/s003350020019
  5. Meyers, S. N., M. B. Rogatcheva, D. M. Larkin, M. Yerle, D. Milan, R. J. Hawken, L. B. Schook and J. E. Beever. 2005. Piggy-BACing the human genome II. A high-resolution, physically anchored, comparative map of the porcine autosomes. Genomics 86(6):739-752. https://doi.org/10.1016/j.ygeno.2005.04.010
  6. Otieno, C. J., J. Bastiaansen, A. M. Ramos and M. F. Rothschild. 2005. Mapping and association studies of diabetes related genes in the pig. Anim. Genet. 36(1):36-42. https://doi.org/10.1111/j.1365-2052.2004.01217.x
  7. 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(1):17-27. https://doi.org/10.1111/j.1365-2052.2005.01368.x
  8. Sato, S., Y. Oyamada, K. Atsuji, T. Nade, S. Sato, E. Kobayashi, T. Mitsuhashi, K. Nirasawa, A. Komatsuda, Y. Saito, S. Terai, T. Hayashi and Y. Sugimoto. 2003. Quantitative trait loci analysis for growth and carcass traits in a Meishan$\times$Duroc F2 resource population. J. Anim. Sci. 81(12):2938-2949. https://doi.org/10.2527/2003.81122938x
  9. Werner, P., S. Neuenschwander and G. Stranzinger. 1999. Characterization of the porcine uncoupling proteins 2 and 3 (UCP2 and UCP3) and their localization to chromosome 9 p by somatic cell hybrids. Anim. Genet. 30(3):221-224. https://doi.org/10.1046/j.1365-2052.1999.00462.x
  10. Ciobanu, D. C., J. W. Bastiaansen, S. M. Lonergan, H. Thomsen, J. C. Dekkers, G. S. Plastow and M. F. Rothschild. 2004. New alleles in calpastatin gene are associated with meat quality traits in pigs. J. Anim. Sci. 82(10):2829-2839. https://doi.org/10.2527/2004.82102829x
  11. Fujii, J., K. Otsu, F. Zorzato, S. de Leon, V. K. Khanna, J. E. Weiler, P. J. O'Brien and D. H. MacLennan. 1991. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Sci. 253:448-451. https://doi.org/10.1126/science.1862346
  12. Goodwin, R. and S. Burroughs. 1995. Genetic evaluation terminal line program results. National Prok Producers Council, Des Moines, Iowa.
  13. Jungerius, B. J., A. P. Rattink, R. P. Crooijmans, J. J. van der Poel, B. A. van Oost, M. F. te Pas and M. A. Groenen. 2003. Development of a single nucleotide polymorphism map of porcine chromosome 2. Anim. Genet. 34(6):429-437. https://doi.org/10.1046/j.0268-9146.2003.01056.x
  14. Kim, J. J., M. F. Rothschild, J. Beever, S. Rodriguez-Zas and J. C. Dekkers. 2005. Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J. Anim. Sci. 83(6):1229-1240. https://doi.org/10.2527/2005.8361229x
  15. van Wijk, H. J., B. Dibbits, E. E. Baron, A. D. Brings, B. Harlizius, M. A. Groenen, E. E. Knol and H. Bovenhuis. 2006. Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross. J. Anim. Sci. 84(4):789-799. https://doi.org/10.2527/2006.844789x
  16. Wimmers, K., I. Fiedler, T. Hardge, E. Murani, K. Schellander and S. Ponsuksili. 2006. QTL for microstructural and biophysical muscle properties and body composition in pigs. BMC Genet. 9:7-15.
  17. Yu, M., B. Geiger, N. Deeb and M. F. Rothschild. 2006. Liver X receptor alpha and beta genes have the potential role on loin lean and fat content in pigs. J. Anim. Breed Genet. 123(2):81-88. https://doi.org/10.1111/j.1439-0388.2006.00576.x
  18. Jin, H. J., B. Y. Park, J. C. Park, I. H. Hwang, S. S. Lee, S. H. Yeon, C. D. Kim, C. Y. Cho, Y. K. Kim, K. S. Min, S. T. Feng, Z. D. Li, C. K. Park and C. I. Kim. 2006. The effects of stress related genes on carcass traits and meat quality in pigs. Asian-Aust. J. Anim. Sci. 19(2):280-285.

Cited by

  1. Analyses of porcine public SNPs in coding-gene regions by re-sequencing and phenotypic association studies vol.38, pp.6, 2011, https://doi.org/10.1007/s11033-010-0496-1