Mammalian Genome

, Volume 19, Issue 6, pp 429–438 | Cite as

Combined line-cross and half-sib QTL analysis in Duroc–Pietrain population

  • Guisheng Liu
  • Jong Joo Kim
  • Elisebeth Jonas
  • Klaus Wimmers
  • Siriluck Ponsuksili
  • Eduard Murani
  • Chirawath Phatsara
  • Ernst Tholen
  • Heinz Juengst
  • Dawit Tesfaye
  • Ji Lan Chen
  • Karl Schellander
Article

Abstract

A Duroc–Pietrain resource population was built to detect quantitative trait loci (QTL) that affect growth, carcass composition, and pork quality. The data were analyzed by applying three least-squares Mendelian models: a line-cross (LC) model, a half-sib (HS) model, and a combined LC and HS model (CB), which enabled the detection of QTL that had fixed, equal, and different allele frequencies for alternate breed alleles, respectively. Permutation tests were performed to determine 5% chromosome-wide and 5% genome-wide threshold values. A total of 40 (137) QTL were detected at the 5% genome-wide (chromosome-wide) level for the 35 traits analyzed. Of the 137 QTL detected, 62 were classified as the LC type (LC-QTL), 47 as the HS type (HS-QTL), and 28 as the CB type (CB-QTL). The results indicate that implementation of a series of model-based framework is not only beneficial to detect QTL, but also provides us with a new and more robust interpretation from which further methodology could be developed.

References

  1. Alfonso L, Haley CS (1998) Power of different F2 schemes for QTL detection in livestock. Anim Sci 66:1–8Google Scholar
  2. 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 33:289–309PubMedCrossRefGoogle Scholar
  3. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedGoogle Scholar
  4. Dekkers J, Kim JJ, Malek M, Thomsen H, Lee H et al (2003) A genome scan to detect QTL affecting growth, composition, and meat quality trait in a Berkshirer × Yorkshire cross. 28th National Swine Improvement Federation Proc, December 4–5, 2003, Des Moines, IAGoogle Scholar
  5. De Koning DJ, Janss LL, Rattink AP, van Oers PA, de Vries BJ et al (1999) Detection of quantitative trait loci for backfat thickness and intramuscular fat content (Sus scrofa). Genetics 152:1679–1690PubMedGoogle Scholar
  6. De Koning DJ, Rattink AP, Harlizius B, van Arendonk JAM, Brascamp EW et al (2000) Genome-wide scan for body composition in pigs reveals important role of imprinting. Proc Natl Acad Sci USA 97:7947–7950PubMedCrossRefGoogle Scholar
  7. De Koning DJ, Harlizius B, Rattink AP, Groenen MA, Brascamp EW (2001) Detection and characterization of quantitative trait loci for meat quality traits in pigs. J Anim Sci 79:2812–2819PubMedGoogle Scholar
  8. De Koning DJ, Pong-Wong R, Varona L, Evans GJ, Giuffra E et al (2003) Full pedigree quantitative trait locus analysis in commercial pigs using variance components. J Anim Sci 81:2155–2163PubMedGoogle Scholar
  9. Estelle J, Mercade A, Noguera JL, Perez-Enciso M, Ovilo C et al (2005) Effect of the porcine IGF2-intron3–G3072A substitution in an outbred Large White population and in an Iberian × Landrace cross. J Anim Sci 83:2723–2728PubMedGoogle Scholar
  10. Evans GJ, Giuffra E, Sanchez A, Kerje S, Davalos G et al (2003) Identification of quantitative trait loci for production traits in commercial pig populations. Genetics 164:621–627PubMedGoogle Scholar
  11. Green P, Falls K, Crooks S (1990) Documentation for CRIMAP version 2.4. Washington University School of Medicine, St. Louis, MOGoogle Scholar
  12. Haley CS, Knott SA, Elsen JM (1994) Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136:1195–1207PubMedGoogle Scholar
  13. Jungerius BJ, Van Laere AS, Te Pas MF, Van Oost BA, Andersson L et al (2004) The IGF2-intron3–G3072A substitution explains a major imprinted QTL effect on backfat thickness in a Meishan European white pig intercross. Genet Res 84:95–101PubMedCrossRefGoogle Scholar
  14. Kim JJ, Rothschild MF, Beever J, Rodriguez-Zas S, Dekkers JCM (2005a) Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. J Anim Sci 83:1229–1240PubMedGoogle Scholar
  15. Kim JJ, Zhao H, Thomsen H, Rothschild MF, Dekkers JCM (2005b) Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet Res 85:235–248PubMedCrossRefGoogle Scholar
  16. Knott SA, Elson JM, Haley CS (1996) Methods for multimarker mapping of quantitative trait loci in half-sib populations. Theor Appl Genet 93:71–80CrossRefGoogle Scholar
  17. Krzecio E, Kuryl J, Kocwin-Podsiadla M, Monin G (2005) Association of calpastatin (CAST/MspI) polymorphism with meat quality parameters of fatteners and its interaction with RYR1 genotypes. J Anim Breed Genet 122:251–258PubMedCrossRefGoogle Scholar
  18. Liu G, Jennen DGJ, Tholen E, Juengst H, Kleinwächter T et al (2007) A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc–Pietrain resource population. Anim Genet 38:241–252PubMedCrossRefGoogle Scholar
  19. Meyers SN, Rodriguez-Zas SL, Beever JE (2007) Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2. BMC Genet 8:69PubMedCrossRefGoogle Scholar
  20. 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 34:705–728PubMedCrossRefGoogle Scholar
  21. Nagamine Y, Haley CS, Sewalem A, Visscher PM (2003) Quantitative trait loci variation for growth and obesity between and within lines of pigs (Sus scrofa). Genetics 164:629–635PubMedGoogle Scholar
  22. Nagamine Y, Visscher PM, Haley CS (2004) QTL detection and allelic effects for growth and fat traits in outbred pig populations. Genet Sel Evol 36:83–96PubMedCrossRefGoogle Scholar
  23. Quackenbush J (2007) Extracting biology from high-dimensional biological data. J Exp Biol 210:1507–1517PubMedCrossRefGoogle Scholar
  24. Quintanilla R, Demeure O, Bidanel JP, Milan D, Iannuccelli N et al (2003) Detection of quantitative trait loci for fat androstenone levels in pigs. J Anim Sci 81:385–394PubMedGoogle Scholar
  25. 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 11:656–661PubMedCrossRefGoogle Scholar
  26. Rohrer GA, Keele J (1998) Identification of quantitative trait loci affecting carcass composition in swine. II. Muscling and wholesale product yield traits. J Anim Sci 76:2255–2262PubMedGoogle Scholar
  27. Rohrer GA, Thallman RM, Shackelford S, Wheeler T, Koohmaraie M (2006) A genome scan for loci affecting pork quality in a Duroc-Landrace F2 population. Anim Genet 37:17–27PubMedCrossRefGoogle Scholar
  28. Su YC, Deng CY, Xiong YZ, Zheng R, Yu L et al (2002) The construction of the genetic map and QTL locating analysis on chromosome 2 in swine. Acta Genet Sin 29(11):972–976PubMedGoogle Scholar
  29. Tribout T, Iannuccelli N, Druet T, Gilbert H, Riquet J et al (2008) Detection of quantitative trait loci for reproduction and production traits in LargeWhite and French Landrace pig populations. Genet Sel Evol 40:61–78PubMedCrossRefGoogle Scholar
  30. van Wijk HJ, Buschbell H, Dibbits B, Liefers SC, Harlizius B et al (2007) Variance component analysis of quantitative trait loci for pork carcass composition and meat quality on SSC4 and SSC11. J Anim Sci 85:22–30PubMedCrossRefGoogle Scholar
  31. Yue G, Stratil A, Cepica S, Schroeffel J Jr, Schroeffelova D et al (2003) Linkage and QTL mapping for Sus scrofa chromosome 7. J Anim Breed Genet 120(1):56–65CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Guisheng Liu
    • 1
    • 2
  • Jong Joo Kim
    • 3
  • Elisebeth Jonas
    • 1
  • Klaus Wimmers
    • 4
  • Siriluck Ponsuksili
    • 4
  • Eduard Murani
    • 4
  • Chirawath Phatsara
    • 1
  • Ernst Tholen
    • 1
  • Heinz Juengst
    • 1
  • Dawit Tesfaye
    • 1
  • Ji Lan Chen
    • 5
  • Karl Schellander
    • 1
  1. 1.Animal Breeding and Husbandry Group, Institute of Animal ScienceUniversity of BonnBonnGermany
  2. 2.Hubei Key Lab of Animal Embryo Engineering and Molecular BreedingInstitute of Animal and Veterinary Science, Hubei Academy of Agricultural ScienceHubei ProvinceChina
  3. 3.School of BiotechnologyYeungnam UniversityGyeongsanKorea
  4. 4.Research Institute for the Biology of Farm Animals (FBN)DummerstorfGermany
  5. 5.Beijing Institute of Animal and Veterinary Science, China Academy of Agricultural ScienceBeijingChina

Personalised recommendations