Molecular Biology Reports

, Volume 39, Issue 4, pp 4101–4110 | Cite as

Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle

  • Ozlem Aslan
  • Ruth M. Hamill
  • Grace Davey
  • Jean McBryan
  • Anne Maria Mullen
  • Marina Gispert
  • Torres Sweeney


Intramuscular fat (IMF) and subcutaneous fat (back fat-BF) are two of the major fat depots in livestock. A QTN located in the insulin-like growth factor 2 gene (IGF2) has been associated with a desirable reduction in BF depth in pigs. Given that the lipid metabolism of intramuscular adipocytes differs from that of subcutaneous fat adipocytes, this study aimed to search for genetic variation in the IGF2 gene that may be associated with IMF, as well as BF, in diverse pig breeds. Four proximal promoter regions of the IGF2 gene were characterised and the association of IGF2 genetic variation with IMF and BF was assessed. Six promoter SNPs were identified in four promoter regions (P1–P4; sequence coverage 945, 866, 784 and 864 bp, respectively) in phenotypically diverse F1 cross populations. Three promoter SNPs were subsequently genotyped in three pure breeds (Pietrain = 98, Duroc = 99 and Large White = 98). All three SNPs were >95% monomorphic in the Pietrain and Duroc breeds but minor alleles were at moderate frequencies in the Large White breed. These SNPs were linked and one was located in a putative transcription factor binding site. Five haplotypes were inferred and three combined diplotypes tested for association with IMF and BF in the Large White. As expected haplotype 1 (likely in LD with the beneficial QTN allele) was superior for BF level. In contrast, the heterozygote diplotype of the most common haplotypes (1 and 2) was associated with higher IMF and marbling scores compared to either homozygote. Gene expression analysis of divergent animals showed that IGF2 was 1.89 fold up-regulated in muscle with higher compared to lower IMF content. These findings suggest that genetic variation in the promoter region of the IGF2 gene is associated with IMF content in porcine skeletal muscle and that greater expression of the IGF2 gene is associated with higher IMF content.


Insulin-like growth factor 2 Subcutaneous Adipose Marbling Polymorphism 



Insulin-like growth factor 2 gene


Single nucleotide polymorphism


Promoter 1


Promoter 2


Promoter 3


Promoter 4


Intramuscular fat


Back fat


Transcription start site


Transcription factor binding site



The authors acknowledge Genus PLC/PIC US for provision of gDNA samples from purebred Large White, Pietrain and Duroc pigs. The authors also wish to thank Ms. Paula Reid, Teagasc for assistance with data analysis. Funding for this research was provided under the National Development Plan, through the Food Institutional Research Measure, administered by the Department of Agriculture, Fisheries & Food, Ireland.

Supplementary material

11033_2011_1192_MOESM1_ESM.doc (34 kb)
Supplementary material 1 (DOC 35 kb)


  1. 1.
    Hausman GJ, Dodson MV, Ajuwon K, Azain M, Barnes KM, Guan LL, Jiang Z, Poulos SP, Sainz RD, Smith S, Spurlock M, Novakofski J, Fernyhough ME, Bergen WG (2009) Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals. J Anim Sci 87:1218–1246PubMedCrossRefGoogle Scholar
  2. 2.
    Kouba M, Bonneau M, Noblet J (1999) Relative development of subcutaneous, intermuscular, and kidney fat in growing pigs with different body compositions. J Anim Sci 77(3):622–629PubMedGoogle Scholar
  3. 3.
    Gao SZ, Zhao SM (2009) Physiology, affecting factors and strategies for control of pig meat intramuscular fat. Recent Pat Food Nutr Agric 1(1):59–74. doi: 10.2174/1876142910901010059 PubMedGoogle Scholar
  4. 4.
    Gerbens F, van Erp AJ, Harders FL, Verburg FJ, Meuwissen TH, Veerkamp JH, te Pas MF (1999) Effect of genetic variants of the heart fatty acid-binding protein gene on intramuscular fat and performance traits in pigs. J Anim Sci 77(4):846–852PubMedGoogle Scholar
  5. 5.
    Hocquette JF, Gondret F, Baéza E, Médale F, Jurie C, Pethick DW (2010) Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, and identification of putative markers. Animal 4(2):303–319. doi: 10.1017/S1751731109991091 CrossRefGoogle Scholar
  6. 6.
    Cho KH, Kim MJ, Jeon GJ, Chung HY (2011) Association of genetic variants for FABP3 gene with back fat thickness and intramuscular fat content in pig. Mol Biol Rep 38(3):2161–2166. doi: 10.1007/s11033-010-0344-3 PubMedCrossRefGoogle Scholar
  7. 7.
    Smith SB, Crouse JD (1984) Relative contributions of acetate, lactate and glucose to lipogenesis in bovine intramuscular and subcutaneous adipose-tissue. J Nutr 114(4):792–800PubMedGoogle Scholar
  8. 8.
    Sellier P (1998) Genetics of meat and carcass traits. In: Rothschild M, Rubinsky A (eds) The genetics of the pig. CAB Int, New York, USA, pp 463–510Google Scholar
  9. 9.
    Suzuki K, Irie M, Kadowaki H, Shibata T, Kumagai M, Nishida A (2005) Genetic parameter estimates of meat quality traits in Duroc pigs selected for average daily gain, longissimus muscle area, backfat thickness, and intramuscular fat content. J Anim Sci 83(9):2058–2065PubMedGoogle Scholar
  10. 10.
    Van Wyk JJ, Smith EP (1999) Insulin-like growth factors and skeletal growth: possibilities for therapeutic interventions. J Clin Endocrinol Metab 84(12):4349–4354PubMedCrossRefGoogle Scholar
  11. 11.
    Pavelic K, Bukovic D, Pavelic J (2002) The role of insulin-like growth factor 2 and its receptors in human tumors. Mol Med 8(12):771–780PubMedGoogle Scholar
  12. 12.
    Li C, Bin Y, Curchoe C, Yang L, Feng D, Jiang Q, O’Neill M, Tian XC, Zhang S (2008) Genetic imprinting of H19 and IGF2 in domestic pigs (Sus scrofa). Anim Biotechnol 19(1):22–27PubMedCrossRefGoogle Scholar
  13. 13.
    Wrzeska M, Zyga A, Rejduch B, Slota E (2006) A note on biallelic expression of the IGF2 gene in the liver and brain of adult pigs. J Anim Feed Sci 15(1):57–60Google Scholar
  14. 14.
    Jeon JT, Carlborg O, Tornsten A, Giuffra E, Amarger V, Chardon P, Andersson-Eklund L, Andersson K, Hansson I, Lundstrom K, Andersson L (1999) A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. Nat Genet 21(2):157–158. doi: 10.1038/5938 PubMedCrossRefGoogle Scholar
  15. 15.
    Nezer C, Moreau L, Brouwers B, Coppieters W, Detilleux J, Hanset R, Karim L, Kvasz A, Leroy P, Georges M (1999) An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat Genet 21(2):155–156. doi: 10.1038/5935 PubMedCrossRefGoogle Scholar
  16. 16.
    Van Laere A, Nguyen M, Braunschwieg M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832–835PubMedCrossRefGoogle Scholar
  17. 17.
    Estelle J, Mercade A, Noguera JL, Perez-Enciso M, Ovilo C, Sanchez A, Folch JM (2005) Effect of the porcine IGF2-intron3-G3072A substitution in an outbred Large White population and in an Iberian × Landrace cross. J Anim Sci 83(12):2723–2728PubMedGoogle Scholar
  18. 18.
    Jungerius BJ, van Laere AS, Te Pas MF, van Oost BA, Andersson L, Groenen MA (2004) The IGF2-intron3-G3072A substitution explains a major imprinted QTL effect on backfat thickness in a Meishan × European white pig intercross. Genet Res 84(2):95–101PubMedCrossRefGoogle Scholar
  19. 19.
    Oczkowicz M, Tyra M, Walinowicz K, Rozycki M, Rejduch B (2009) Known mutation (A3072G) in intron 3 of the IGF2 gene is associated with growth and carcass composition in Polish pig breeds. J Appl Genet 50(3):257–259PubMedCrossRefGoogle Scholar
  20. 20.
    Gardan D, Gondret F, Louveau I (2006) Lipid metabolism and secretory function of porcine intramuscular adipocytes compared with subcutaneous and perirenal adipocytes. Am J Physiol-Endoc M 291(2):E372–E380Google Scholar
  21. 21.
    Gardan D, Gondret F, Van den Maagdenberg K, Buys N, De Smet S, Louveau I (2008) Lipid metabolism and cellular features of skeletal muscle and subcutaneous adipose tissue in pigs differing in IGF-II genotype. Domest Anim Endocrin 34(1):45–53CrossRefGoogle Scholar
  22. 22.
    Bahar B, Sweeney T (2008) Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene. BMC Genetics 9:91. doi: 10.1186/1471-2156-9-91 PubMedCrossRefGoogle Scholar
  23. 23.
    Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2(4):e30. doi: 10.1371/journal.pgen.0020030 PubMedCrossRefGoogle Scholar
  24. 24.
    Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424(6945):147–151. doi: 10.1038/nature01763 PubMedCrossRefGoogle Scholar
  25. 25.
    Planas J, Serrat JM (2010) Gene promoter evolution targets the center of the human protein interaction network. PLoS One 5(7):e11476. doi: 10.1371/journal.pone.0011476 PubMedCrossRefGoogle Scholar
  26. 26.
    Roni V, Carpio R, Wissinger B (2007) Mapping of transcription start sites of human retina expressed genes. BMC Genomics 8:42. doi: 10.1186/1471-2164-8-42 PubMedCrossRefGoogle Scholar
  27. 27.
    Aslan O, Sweeney T, Mullen AMM, Hamill RM (2010) Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content. BMC Genetics 11(111):1–14. doi: 10.1186/1471-2156-11-111 Google Scholar
  28. 28.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599. doi: 10.1093/molbev/msm092 PubMedCrossRefGoogle Scholar
  29. 29.
    Plastow GS, Carrion D, Gil M, Garcia-Regueiro JA, Furnols MFI, Gispert M, Oliver MA, Velarde A, Guardia MD, Hortos M, Rius MA, Sarraga C, Diaz I, Valero A, Sosnicki A, Klont R, Dornan S, Wilkinson JM, Evans G, Sargent C, Davey G, Connolly D, Houeix B, Maltin CM, Hayes HE, Anandavijayan V, Foury A, Geverink N, Cairns M, Tilley RE, Mormede P, Blott SC (2005) Quality pork genes and meat production. Meat Sci 70(3):409–421. doi: 10.1016/j.meatsci.2004.06.025 PubMedCrossRefGoogle Scholar
  30. 30.
    Gispert M, Font i Furnols M, Gil M, Velarde A, Diestre A, Carrión D, Sosnicki A, Plastow G (2007) Relationships between carcass quality parameters and genetic types. Meat Sci 77(3):397–404PubMedCrossRefGoogle Scholar
  31. 31.
    NPPC (1999) National Pork Producers Council. Des Moines, Iowa, USAGoogle Scholar
  32. 32.
    Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265. doi: 10.1093/bioinformatics/bth457 PubMedCrossRefGoogle Scholar
  33. 33.
    Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50Google Scholar
  34. 34.
    Version 9.1 SI, Inc., Cary, NC (2002–2003) SASGoogle Scholar
  35. 35.
    Bostian M, Fish D, Webb N, Arey J (1985) Automated methods for determination of fat and moisture in meat and poultry products: collaborative study. J Assoc Off Anal Chem 68:876–880PubMedGoogle Scholar
  36. 36.
    Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45PubMedCrossRefGoogle Scholar
  37. 37.
    Stirling D, Stear MJ (2010) g you The direct determination of haplotypes from extended regions of genomic DNA. BMC Genomics 11:223. doi: 10.1186/1471-2164-11-223
  38. 38.
    Tan Q, Christiansen L, Christensen K, Bathum L, Li S, Zhao JH, Kruse TA (2005) Haplotype association analysis of human disease traits using genotype data of unrelated individuals. Genet Res 86(3):223–231PubMedCrossRefGoogle Scholar
  39. 39.
    Li J, Zhou Y, Elston RC (2006) Haplotype-based quantitative trait mapping using a clustering algorithm. BMC Bioinform 7:258. doi: 10.1186/1471-2105-7-258 CrossRefGoogle Scholar
  40. 40.
    Wang YH, Byrne KA, Reverter A, Harper GS, Taniguchi M, McWilliam SM, Mannen H, Oyama K, Lehnert SA (2005) Transcriptional profiling of skeletal muscle tissue from two breeds of cattle. Mammalian Genome 16(3):201–210. doi: 10.1007/s00335-004-2419-8 PubMedCrossRefGoogle Scholar
  41. 41.
    Wang X, Tomso DJ, Chorley BN, Cho HY, Cheung VG, Kleeberger SR, Bell DA (2007) Identification of polymorphic antioxidant response elements in the human genome. Hum Mol Genet 16(10):1188–1200. doi: 10.1093/hmg/ddm066 PubMedCrossRefGoogle Scholar
  42. 42.
    Chorley BN, Wang X, Campbell MR, Pittman GS, Noureddine MA, Bell DA (2008) Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat Res/Rev Mutat Res 659(1–2):147–157. doi: 10.1016/j.mrrev.2008.05.001 Google Scholar
  43. 43.
    Davoli R, Braglia S (2008) Molecular approaches in pig breeding to improve meat quality. Briefings in Functional Genomics and Proteomics Advance Access January 21, 2008:1–9Google Scholar
  44. 44.
    Vykoukalova Z, Knoll A, Dvorak J, Cepica S (2006) New SNPs in the IGF2 gene and association between this gene and backfat thickness and lean meat content in Large White pigs. J Anim Breed Genet 123(3):204–207PubMedCrossRefGoogle Scholar
  45. 45.
    Dalca AV, Brudno M (2010) Genome variation discovery with high-throughput sequencing data. Brief Bioinform 11(1):3–14PubMedCrossRefGoogle Scholar
  46. 46.
    Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10(3):R32. doi: 10.1186/gb-2009-10-3-r32 PubMedCrossRefGoogle Scholar
  47. 47.
    Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA (2010) Heterosis. Plant Cell 22(7):2105–2112. doi: 10.1105/tpc.110.076133 PubMedCrossRefGoogle Scholar
  48. 48.
    Van den Brand H, Kemp B (2006) Dietary fat and reproduction in the post partum sow. Soc Reprod Fertil Suppl 62:177–189PubMedGoogle Scholar
  49. 49.
    Zhao GP, Chen JL, Zheng MQ, Wen J, Zhang Y (2007) Correlated responses to selection for increased intramuscular fat in a Chinese quality chicken line. Poult Sci 86(11):2309–2314PubMedGoogle Scholar
  50. 50.
    Badinga L, Song S, Simmen RC, Clarke JB, Clemmons DR, Simmen FA (1999) Complex mediation of uterine endometrial epithelial cell growth by insulin-like growth factor-II (IGF-II) and IGF-binding protein-2. J Mol Endocrinol 23(3):277–285PubMedCrossRefGoogle Scholar
  51. 51.
    Schams D, Berisha B, Kosmann M, Einspanier R, Amselgruber WM (1999) Possible role of growth hormone, IGFs, and IGF-binding proteins in the regulation of ovarian function in large farm animals. Domest Anim Endocrin 17(2–3):279–285CrossRefGoogle Scholar
  52. 52.
    Berkowicz EW, Magee DA, Sikora KM, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, Machugh DE (2010) Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle. J Dairy Res 1–8. doi: 10.1017/S0022029910000567
  53. 53.
    Muñoz M, Fernández A, Ovilo C, Muñoz G, Rodriguez C, Fernández A, Alves E, Silió L (2010) Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line. Genet Sel Evol 42:23. doi: 10.1186/1297-9686-42-23 PubMedCrossRefGoogle Scholar
  54. 54.
    Kim JJ, Zhao H, Thomsen H, Rothschild MF, Dekkers JC (2005) Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet Res 85(3):235–248PubMedCrossRefGoogle Scholar
  55. 55.
    Thomsen H, Lee HK, Rothschild MF, Malek M, Dekkers JC (2004) Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. J Anim Sci 82(8):2213–2228PubMedGoogle Scholar
  56. 56.
    Sanchez MP, Riquet J, Iannuccelli N, Gogue J, Billon Y, Demeure O, Caritez JC, Burgaud G, Feve K, Bonnet M, Pery C, Lagant H, Le Roy P, Bidanel JP, Milan D (2006) Effects of quantitative trait loci on chromosomes 1, 2, 4, and 7 on growth, carcass, and meat quality traits in backcross Meishan × Large White pigs. J Anim Sci 84(3):526–537PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Ozlem Aslan
    • 1
    • 2
  • Ruth M. Hamill
    • 1
  • Grace Davey
    • 3
  • Jean McBryan
    • 1
  • Anne Maria Mullen
    • 1
  • Marina Gispert
    • 4
  • Torres Sweeney
    • 2
  1. 1.Teagasc Food Research CentreAshtown, Dublin 15Ireland
  2. 2.UCD School of Agriculture, Food Science & Veterinary MedicineBelfield, Dublin 4Ireland
  3. 3.Functional Genomics and Glycomics Group, Martin Ryan Institute, National University of IrelandGalwayIreland
  4. 4.IRTA-MonellsMonells, GironaSpain

Personalised recommendations