Potential of the Quantitative Trait Loci Mapping Using Crossbred Population

Yang, Shulin;Zhu, Zhengmao;Li, Kui

  • Received : 2004.09.26
  • Accepted : 2005.05.17
  • Published : 2005.12.01


In the process of crossbreeding, the linkage disequilibria between the quantitative trait loci (QTL) and their linked markers were reduced gradually with increasing generations. To study the potential of QTL mapping using the crossbred population, we presented a mixed effect model that treated the mean allelic value of the different founder populations as the fixed effect and the allelic deviation from the population mean as random effect. It was assumed that there were fifty QTLs having effect on the trait variation, the population mean and variance were divided to each QTL in founder generation in our model. Only the additive effect was considered in this model for simulation. Six schemes (S1-S6) of crossbreeding were studied. The selection index was used to evaluate the synthetic breeding value of two traits of the individual in the scheme of S2, S4 and S6, and the individuals with high selection index were chosen as the parents of the next generation. Random selection was used in the scheme of S1, S3 and S5. In this study, we premised a QTL explained 40% of the genetic variance was located in a region of 20 cM by the linkage analysis previously. The log likelihood ratio (log LR) was calculated to determine the presence of a QTL at the particular chromosomal position in each of the generations from the fourth to twentieth. The profiles of log LR and the number of the highest log LR located in the region of 5, 10 and 20 cM were compared between different generations and schemes. The profiles and the correct number reduced gradually with the generations increasing in the schemes of S2, S4 and S6, but both of them increased in the schemes of S1, S3 and S5. From the results, we concluded that the crossbreeding population undergoing random selection was suitable for improving the resolution of QTL mapping. Even experiencing index selection, there was still enough variation existing within the crossbred population before the fourteenth generation that could be used to refine the location of QTL in the chromosome region.


Crossbred Population;Index Selection;Linkage Disequilibrium;QTL Mapping


  1. Farnir, F., B. Grisart, W. Coppieters, J. Riquet, P. Berzi, N. Cambisano, L. Karim, M. Mni, S. Moisio, P. Simon, D. Wagenaar, J. Vilkki and M. Georges. 2002. Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect milk production on bovine chromosome 14. Genet. 161:275-287.
  2. Grignola, F. E., I. Hoeschele and B. Tier. 1996a. Mapping quantitative trait loci via Residual Maximum Likelihood: I. Methodology. Genet. Sel. Evol. 28:479-490.
  3. Kao, C. H., Z. B. Zeng and R. D. Teasdale. 1999. Multiple interval mapping for quantitative trait loci. Genet. 152:1203-1216.
  4. Meuwissen, T. H. E. and M. E. Goddard. 2000. Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci. Genet. 155:421-430.
  5. Patterson, H. D. and R. Thompson. 1971. Recovery of inter-block information when block sizes are unequal. Biometrika. 58:545-554.
  6. Pritchard, C., D. R. Cox and R. M. Myers. 1991. The end in sight for Huntington disease, Am. J. Hum. Genet. 49:1-6.
  7. Wang, T., R. L. Fernando, S. Van der Beek, M. Grossman and J. A. M. Van Arendonk. 1995. Covariance between relatives for a marked quantitative trait locus. Genet. Sel. Evol. 27:251-274.
  8. Zeng, Z. B. 1994. Precision mapping of quantitative trait loci. Genet. 136:1457-1468.
  9. Darvasi, A. and M. Soller. 1995. Advanced intercross lines, an experimental population for fine genetic mapping. Genet. 141:1199-1207.
  10. Grignola, F. E., I. Hoeschele, Q. Zhang and B. Tier. 1996b. Mapping quantitative trait loci via Residual Maximum likelihood: II. A simulation study. Genet. Sel. Evol. 28:491-804.
  11. Haldane, J. B. S. 1919. The combination of linkage values and the calculation of diatances between the loci of linked factors. J. Genet. 8:299-309.
  12. Hill, W. G. 1998. Selection with recurrent backcrossing to develop congenic lines for quantitative trait loci analysis. Genet. 148:1341-1352.
  13. Luo, Z. W., C. I. Wu and M. J. Kearsey. 2002. Precision and highresolution mapping of quantitative trait loci by use of recurrent selection, backcross or intercross schemes. Genet. 161:915-929.
  14. Riquet, J., W. Coppieters, N. Cambisano, J. Arranz, P. Berzi, S. K. Davis, B. Grisart, F. Farnir, L. Karim, M. Mnim, P. Simon, J. F. Taylor, P. Vanmanshoven, D. Wagenaar, J. E. Womack and M. Georges. 1999. Fine-mapping of quantitative trait loci by identity by descent in outbred populations: Application to milk production in dairy cattle. Proc. Natl. Acad. Sci. USA. 96:9252-9257.
  15. Zuo, B., Y. Z. Xiong, Y. H. Su, C. Y. Deng, M. G. Lei, R. Zheng, S. W. Jiang and F. E. Li. 2004. Mapping of quantitative trait loci on porcine chromosome 7 using combined data analysis. Asian-Aust. J. Anim. Sci. 17(10):1350-1354
  16. Fernando, R. L. and M. Grossman. 1989. Marker-asssisted selection using best linear unbiased prediction. Genet. Sel. Evol. 21:467-477.
  17. Hayes, B. and M. E. Goddard. 2001. The distribution of the effects of genes affecting quantitative traits in livestock. Genet. Sel. Evol. 33:209-229.
  18. Mott, R., C. J. Talbot, M. G. Turri, A. C. Collins and J. Flint. 2002b. From the cover: a method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl. Acad. Sci. USA 97:12649-12654.
  19. Mott, R. and J. Flint. 2002a. Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks. Genet. 160:1609-1618.
  20. Grignola, F. E., Q. Zhang and I. Hoeschele. 1997. Mapping linked quantitative trait loci via Residual Maximum Likelihood. Genet. Sel. Evol. 29:529-544.
  21. Graser, H. U., S. P. Smith and B. Tier. 1987. A derivative-free approach for estimating variance components in animal models by restricted maximum likelihood. J. Anim. Sci. 64:1362-1370.
  22. Lee, C. Y. and X. L. Wu. 2003. Evaluation of Cofactor Markers for Controlling Genetic Background Noise in QTL Mapping. Asian-Aust. J. Anim. Sci. 16(3):473-480.
  23. Meuwissen, T. H. E., A. Karlsen, S. Lien, I. Olsaker and M. E. Goddard. 2002. Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genet. 161:373-379.
  24. Spielman, R. S. and W. J. Ewens. 1996. The TDT and other family traits based tests for linkage disequilibrium and association. Am. J. Hum. Genet. 59:983-989.
  25. Zeng, Z. B. 1993. Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc. Natl. Acad. Sci. USA. 90:10972-10976.
  26. Abdel-Azim, G. and A. E. Freeman. 2001. A rapid method for computing the inverse of the genetic covariance matrix between relatives for a marked Quantitative Trait Locus. Genet. Sel. Evol. 33:153-174.
  27. Wright, S. 1952. Quantitative inheritance, Her Majesty’s Stationery Office, Lodon.
  28. Nagamine, Y., C. S. Haley, A. Sewalem and P. M. Visscher. 2003. Quantitative Trait Loci variation for growth and obesity between and within lines of pigs. Genet. 164:629-635.
  29. Evans, G. J., E. Giuffra, A. Sanchez, S. Kerje, G. Davalos, O. Vidal, S. Illaí, J. L. Noguera, L. Varona, I. Velander, O. I. Southwood, D. J. de Koning, C. S. Haley, G. S. Plastow and L. Andersson. 2003. Identification of Quantitative Trait Loci for Production Traits in Commercial Pig Populations. Genet. 164:621-627.
  30. Yi, N. J. and S. Z. Xu. 2001. Bayesian mapping of quantitative trait loci under complicated mating designs. Genet. 157:1759-1771.
  31. Lee, G. W. 2005. Association of Marker Loci and QTL from Crosses of Inbred Parental Lines. Asian-Aust. J. Anim. Sci. 18(6):772-779.
  32. Haley, C. S. and S. A. Knott. 1992. A simple regression method for interval mapping in line crosses. Heredity 69:315-321.
  33. Hill, W. G. 1997. The use of selection experiments for detecting quantitative trait loci, Genet. Res. 69:227-232.