Mammalian Genome

, Volume 16, Issue 5, pp 374–382 | Cite as

On growth, fatness, and form: A further look at porcine Chromosome 4 in an Iberian × Landrace cross

  • Anna Mercadé
  • Jordi Estellé
  • José L. Noguera
  • Josep M. Folch
  • Luis Varona
  • Luis Silió
  • Armand Sánchez
  • Miguel Pérez-Enciso
Article

Abstract

A crossed population between Iberian × Landrace pigs consisting of 321 F2, 87 F3, and 85 backcross individuals has been analyzed to refine the number and positions of quantitative trait loci (QTL) affecting shape, growth, fatness, and meat quality traits in SSC4. A multitrait multi-QTL approach has been used. Our results suggest that carcass length and shoulder weight are affected by two loci. The first one, close to the AFABP gene, has a very strong pleiotropic effect on fatness, whereas the second one, in the interval between S0073 and S0214, also affects live weight, although to a lesser extent. This latter QTL would correspond to the FAT1 locus described initially in pigs. It seems that SSC4’s loci play an important role in redistributing total weight, and the Landrace allele increases shoulder weight and carcass length much more than ham or total weight. Furthermore, there is also strong evidence of additional loci influencing pH and color in more distant, telomeric positions.

Notes

Acknowledgments

This project was funded by Ministerio de Ciencia y Tecnologia (MCYT) (AGF99−0284-CO2) and (CPE03-010) grants. A. Mercadé was funded by a Formació Personal Investigador (FI) fellowship from the Generalitat de Catalunya, and J. Estellé was funded by a Formación Personal Universitario (FPU) grant from the Spanish Ministry of Education and Science (MEC). Part of the analyses was carried out in the Centre de Supercomputació de Catalunya (CESCA).

References

  1. Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M, et al. (1994) Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263, 1771–1774PubMedGoogle Scholar
  2. Ausubel F, Brent R, Kingston R, Moore D, Seidman J, et al. (1987) Current protocols in molecular biology. (New York: Greene Publishing Associates and Wiley-Interscience)Google Scholar
  3. Bidanel JP, Milan D, Iannuccelli N, Amigues Y, Boscher MY, et al. (2001) Detection of quantitative trait loci for growth and fatness in pigs. Genet Sel Evol 33, 289–309CrossRefPubMedGoogle Scholar
  4. Bidanel JP, Rothschild M (2002) Current status of quantitative trait locus mapping in pigs. Pig News and Information 23, 39–54Google Scholar
  5. Clop A, Cercos A, Tomas A, Pérez–Enciso M, Varona L, et al. (2002) Assignment of the 2,4-dienoyl-CoA reductase (DECR) gene to porcine chromosome 4. Anim Genet 33, 164–165CrossRefPubMedGoogle Scholar
  6. Darvasi A (1998) Experimental strategies for the genetic dissection of complex traits in animal models. Nat Genet 18, 19–24CrossRefPubMedGoogle Scholar
  7. De Koning DJ, Janss LL, Rattink AP, van Oers PA, de Vries BJ, et al. (1999) Detection of quantitative trait loci for back fat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics 152, 1679–1690PubMedGoogle Scholar
  8. De Koning DJ, Rattink AP, Harlizius B, Groenen MAM, Brascamp EW, et al. (2001) Detection and characterization of quantitative trait loci for growth and reproduction traits in pigs. Livest Prod Sci 72, 185–198CrossRefGoogle Scholar
  9. Frary A, Fritz L, Tanksley S (2004) A comparative study of the genetic bases of natural variation in tomato leaf, sepal, and petal morphology. Theor Appl Genet 109, 523–533CrossRefPubMedGoogle Scholar
  10. Gilbert H, Le Roy P (2003) Comparison of three multitrait methods for QTL detection. Genet Sel Evol 35; 281–304CrossRefPubMedGoogle Scholar
  11. Green P, Falls K, Crooks S (1990) Documentation for CRIMAP. Unpublished mimeo. Available at: http ://biobase.dk/Embnetut/Crimap/Google Scholar
  12. Iannuccelli N, Woloszyn N, Arhainx J, Gellin J, Milan D (1996) GEMMA: a database to manage and automate microsatellite genotyping. In Proceeding of the International Society of Animal Genetics Conference, Tours, France. (Oxford, UK: Blackwell) p 88Google Scholar
  13. Jonsson P (1975) Methods of pig improvement through breeding in the European countries: A review. Livest Prod Sci 2, 1–28CrossRefGoogle Scholar
  14. Klingenberg CP, Leamy LJ, Routman EJ, Cheverud JM (2001) Genetic architecture of mandible shape in mice: Effects of quantitative trait loci analyzed by geometric morphometrics. Genetics 157, 785–802PubMedGoogle Scholar
  15. Knott SA, Haley CS (2000) Multitrait least squares for quantitative trait loci detection. Genetics 156, 899–911PubMedGoogle Scholar
  16. Knott SA, Marklund L, Haley CS, Andersson K, Davies W, et al. (1998) Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 149, 1069–1080PubMedGoogle Scholar
  17. Knott SA, Nystrom PE, Anderssoneklund L, Stern S, Marklund L, et al. (2002) Approaches to interval mapping of QTL in a multigeneration pedigree: the example of porcine chromosome 4. Anim Genet 33, 26– 32CrossRefPubMedGoogle Scholar
  18. Marklund L, Nystrom PE, Stern S, Andersson–Eklund L, Andersson L (1999) Confirmed quantitative trait loci for fatness and growth on pig chromosome 4. Heredity 82(Pt 2), 134–141CrossRefPubMedGoogle Scholar
  19. Milan D, Bidanel JP, Iannuccelli N, Riquet J, Amigues Y, et al. (2002) Detection of quantitative trait loci for carcass composition traits in pigs. Genet Sel Evol 34, 705–728CrossRefPubMedGoogle Scholar
  20. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16, 1215PubMedGoogle Scholar
  21. Moller M, Berg F, Riquet J, Pomp D, Archibald A, et al. (2004) High-resolution comparative mapping of pig Chromosome 4, emphasizing the FAT1 region. Mamm Genome 15, 717–731CrossRefPubMedGoogle Scholar
  22. Ovilo C, Pérez–Enciso M, Barragan C, Clop A, Rodriguez C, et al. (2000) A QTL for intramuscular fat and back fat thickness is located on porcine chromosome 6. Mamm Genome 11, 344–346CrossRefPubMedGoogle Scholar
  23. Ovilo C, Clop A, Noguera JL, Oliver MA, Barragan C, et al. (2002) Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 pig population. J Anim Sci 80, 2801–2808PubMedGoogle Scholar
  24. Paszek AA, Wilkie PJ, Flickinger GH, Rohrer GA, Alexander LJ, et al. (1999) Interval mapping of growth in divergent swine cross. Mamm Genome 10, 117–122CrossRefPubMedGoogle Scholar
  25. Pérez–Enciso M, Misztal I (2004) Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 20, 2792–2798CrossRefPubMedGoogle Scholar
  26. Pérez–Enciso M, Clop A, Noguera JL, Ovilo C, Coll A, et al. (2000) A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. J Anim Sci 78, 2525–2531PubMedGoogle Scholar
  27. Rattink AP, De Koning DJ, Faivre M, Harlizius B, van Arendonk JA, et al. (2000) Fine mapping and imprinting analysis for fatness trait QTLs in pigs. Mamm Genome 11, 656–661CrossRefPubMedGoogle Scholar
  28. Serra X, Gil F, Pérez–Enciso M, Oliver MA, Vázquez JM, et al. (1998) A comparison of carcass, meat quality and histochemical characteristics of Iberian and Landrace pigs. Livest Prod Sci 56, 215–223CrossRefGoogle Scholar
  29. Turri MG, DeFries JC, Henderson ND, Flint J (2004) Multivariate analysis of quantitative trait loci influencing variation in anxiety-related behavior in laboratory mice. Mamm Genome 15, 69–76CrossRefPubMedGoogle Scholar
  30. Varona L, Ovilo C, Clop A, Noguera JL, Pérez–Enciso M, et al. (2002) QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genet Res 80: 145-154CrossRefPubMedGoogle Scholar
  31. Varona L, Gomez–Raya L, Rauw WM, Clop A, Ovilo C, et al. (2004) Derivation of a Bayes factor to distinguish between linked or pleiotropic quantitative trait loci. Genetics 166, 1025–1035PubMedGoogle Scholar
  32. Walling GA, Archibald AL, Cattermole JA, Downing AC, Finlayson HA, et al. (1998) Mapping of quantitative trait loci on porcine chromosome 4. Anim Genet 29, 415–424CrossRefPubMedGoogle Scholar
  33. Walling GA, Visscher PM, Andersson L, Rothschild MF, Wang L, et al. (2000) Combined analyses of data from quantitative trait loci mapping studies. Chromosome 4 effects on porcine growth and fatness. Genetics 155, 1369–1378PubMedGoogle Scholar
  34. Wang L, Yu TP, Tuggle CK, Liu HC, Rothschild MF (1998) A directed search for quantitative trait loci on chromosomes 4 and 7 in pigs. J Anim Sci 76, 2560–2567PubMedGoogle Scholar
  35. Wu R, Ma CX, Littell RC, Casella G (2002) A statistical model for the genetic origin of allometric scaling laws in biology. J Theor Biol 219, 121–135PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Anna Mercadé
    • 1
  • Jordi Estellé
    • 1
  • José L. Noguera
    • 2
  • Josep M. Folch
    • 1
  • Luis Varona
    • 2
  • Luis Silió
    • 3
  • Armand Sánchez
    • 1
  • Miguel Pérez-Enciso
    • 1
    • 4
  1. 1.Departament de Ciència Animal i dels Aliments, Facultat de VeterinàriaUniversitat Autònoma de BarcelonaBellaterraSpain
  2. 2.Àrea de Producció AnimalCentre Udl-IRTALleidaSpain
  3. 3.Àrea de Genética y Mejora AnimalSGIT-INIAMadridSpain
  4. 4.Institut Català de Recerca i Estudis AvançatsBarcelonaSpain

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