A Novel Single Nucleotide Polymorphism of the Leptin Receptor Gene Associated with Backfat Thickness in Duroc Pigs

두록 돼지의 등지방두께와 연관된 렙틴수용체 유전자의 신규 SNP 마커

Lee, Kyung-Tai;Lee, Hae-Young;Choi, Bong-Hwan;Kim, Jong-Joo;Kim, Tae-Hun

  • Received : 2015.07.23
  • Accepted : 2015.09.21
  • Published : 2016.01.30


Fatness is one of the most important economic traits in pigs. The leptin receptor (LEPR) gene may be a potential candidate for the fatness quantitative trait locus (QTL) on porcine chromosome 6, due to its position and physiological role. Thus, this study was carried out to evaluate the associations between structural variants in the LEPR gene and economic traits in pigs. We obtained an approximately 114-kb sequence containing the complete genomic DNA of the porcine LEPR gene, using shotgun sequencing of a bacterial artificial chromosome clone. We report the complete genomic structure of the porcine LEPR gene. Dozens of transcription factor-binding sites were found in the 1.2 kb upstream region from the transcription start point. An association study was performed with 550 Duroc pigs for 24 single-nucleotide polymorphisms (SNPs), including 6 SNPs within exons and 18 SNPs within the putative 5‘ regulatory region of the porcine LEPR gene. Among them, one SNP (−790C/G) was significantly associated with backfat thickness and lean meat percentage, whereas the others, including two SNPs with missense polymorphisms, had no effect on any phenotype. These results suggest that SNP −790C/G may be a useful marker for genetic improvements of fatness and leanness in Duroc pigs.


Economic trait;leptin receptor;pig;single nucleotide polymorphism


  1. Gerbens, F., de Koning, D. J., Harders, F. L., Meuwissen, T. H., Janss, L. L., Groenen, M. A., Veerkamp, J. H., Van Arendonk, J. A. and te Pas, M. F. 2000. The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs. J. Anim. Sci. 78, 552-559.
  2. de Koning, D. J., Rattink, A. P., Harlizius, B., van Arendonk, J. A., Brascamp, E. W. and Groenen, M. A. 2000. Genome-wide scan for body composition in pigs reveals important role of imprinting. Proc. Natl. Acad. Sci. USA 97, 7947-7950.
  3. Friedman, J. M. and Halaas J. L. 1998. Leptin and the regulation of body weight in mammals. Nature 395, 763-770.
  4. Friedman, J. M. 2002. The function of leptin in nutrition, weight, and physiology. Nutr. Rev. 60, 85-87.
  5. Arnyasi, M., Grindflek, E., Javor, A. and Lien, S. 2006. Investigation of two candidate genes for meat quality traits in a quantitative trait locus region on SSC6: the porcine short heterodimer partner and heart fatty acid binding protein genes. J. Anim. Breed. Genet. 123, 198-203.
  6. Mackowski, M., Szymoniak, K., Szydlowski, M., Kamyczek, M., Eckert, R., Rozycki, M. and Switonski, M. 2005. Missense mutations in exon 4 of the porcine LEPR gene encoding extracellular domain and their association with fatness traits. Anim. Genet. 36, 135-137.
  7. Malek, M., Dekkers, J. C., Lee, H. K., Baas, T. J., Prusa, K., Huff-Lonergan, E. and Rothschild, M. F. 2001. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mamm. Genome 12, 637-645.
  8. Miller, S. G., De Vos, P., Guerre-Millo, M., Wong, K., Hermann, T., Staels, B., Briggs, M. R. and Auwerx, J. 1996. The adipocyte specific transcription factor C/ EBPalpha modulates human ob gene expression. Proc. Natl. Acad. Sci. USA 93, 5507-5511.
  9. Chen, C. C., Chang, T. and Su, H. Y. 2004. Characterization of porcine leptin receptor polymorphisms and their association with reproduction and production traits. Anim. Biotechnol. 15, 89-102.
  10. Gong, D. W., Bi, S., Pratley, R. E. and Weintraub, B. D. 1996. Genomic structure and promoter analysis of the human obese gene. J. Biol. Chem. 271, 3971-3974.
  11. Ovilo, C., Oliver, A., Noguera, J. L., Clop, A., Barragan, C., Varona, L., Rodriguez, C., Toro, M., Sanchez, A., Perez-Enciso, M. and Silio, L. 2002. Test for positional candidate genes for body composition on pig chromosome 6. Genet. Sel. Evol. 34, 465-479.
  12. Ovilo, C., Clop, A., Noguera, J. L., Oliver, M. A., Barragan, C., Rodriguez, C., Silio, L., Toro, M. A., Coll, A., Folch, J. M., Sanchez, A., Babot, D. and Varona, L. 2002. Quantitative trait locus mapping for meat quality traits in an Iberian xLandrace F2 pig population. J. Anim. Sci. 80, 2801-2808.
  13. Ovilo, C., Fernandez, A., Noguera, J. L., Barragan, C., Leton, R., Rodriguez, C., Mercade, A., Alves, E., Folch, J. M., Varona, L. and Toro, M. 2005. Fine mapping of porcine chromosome6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genet. Res. 85, 57-67.
  14. Grindflek, E., Szyda, J., Liu, Z. and Lien, S. 2001. Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross. Mamm. Genome 12, 299-304.
  15. Jacob, M. and Gallinaro, H. 1989. The 5’ splice site: phylogenetic evolution and variable geometry of association with U1RNA. Nucleic Acids Res. 11, 2159-2180.
  16. Jeon, J. T., Park, E. W., Jeon, H. J., Kim, T. H., Lee, K. T. and Cheong, I. C. 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.
  17. Kim, J. J., Rothschild, M. F., Beever, J., Rodriguez-Zas, S. and Dekkers, J. C. M. 2005. Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J. Anim. Sci. 83, 1229-1240.
  18. Muñoz, G., Ovilo, C., Silió, L., Tomás, A., Noguera, J. L. and Rodríguez, M. C. 2009. Single- and joint-population analyses of two experimental pig crosses to confirm quantitative trait loci on Sus scrofa chromosome 6 and leptin receptor effects on fatness and growth traits. J. Anim. Sci. 87, 459-468.
  19. Uemoto, Y., Kikuchi, T., Nakano, H., Sato, S., Shibata, T., Kadowaki, H., Katoh, K., Kobayashi, E. and Suzuki, K. 2012. Effects of porcine leptin receptor gene polymorphisms on backfat thickness, fat area ratios by image analysis, and serum leptin concentrations in a Duroc purebred population. Anim. Sci. J. 83, 375-385.
  20. Uleberg, E., Wideroe, I. S., Grindflek, E., Szyda, J., Lien, S. and Meuwissen, T. H. 2005. Fine mapping of a QTL for intramuscular fat on porcine chromosome 6 using combined linkage and linkage disequilibrium mapping. J. Anim. Breed Genet. 122, 1-6.
  21. Muñoz, G., Alcázar, E., Fernández, A., Barragán, C., Carrasco, A., de Pedro, E., Silió, L., Sánchez, J. L. and Rodríguez, M. C. 2010. Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc × Iberian crossbred pigs. Meat Sci. 88, 169-173.
  22. Ovilo, C., Pérez-Enciso, M., Barragán, C., Clop, A., Rodríquez, C., Oliver, M. A., Toro, M. A. and Noruera, J. L. 2000. A QTL for intramuscular fat and backfat thickness is located on porcine chromosome 6. Mamm. Genome 11, 344-346.
  23. Qian, H., Hausman, G. J., Compton, M. M., Azain, M. J., Hartzell, D. L. and Baile, C. A. 1998. Leptin regulation of peroxisome proliferator-activated receptor-gamma, tumor necrosis factor, and uncoupling protein-2 expression in adipose tissues. Biochem. Biophys. Res. Commun. 246, 660-667.
  24. Sampath, H. and Ntambi, J. M. 2005. Polyunsaturated fatty acid regulation of genes of lipid metabolism. Annu. Rev. Nutr. 25, 317-340.
  25. Tartaglia, L. A., Dembski, M., Weng, X., Deng, N., Culpepper, J., Devos, R., Richards, G. J., Campfield, L. A., Clark, F. T., Deeds, J., Muir, C., Sanker, S., Moriarty, A., Moore, K. J., Smutko, J. S., Mays, G. G., Wool, E. A., Monroe, C. A. and Tepper, R. I. 1995. Identification and expression cloning of a leptin receptor, OB-R. Cell 83, 1263-1271.