Methodology of Mapping Quantitative Trait Loci for Binary Traits in a Half-sib Design Using Maximum Likelihood

Yin, Zongjun;Zhang, Qin;Zhang, Jigang;Ding, Xiangdong;Wang, Chunkao

  • Received : 2004.09.26
  • Accepted : 2005.05.18
  • Published : 2005.12.01


Maximum likelihood methodology was applied to analyze the efficiency and statistical power of interval mapping by using a threshold model. The factors that affect QTL detection efficiency (e.g. QTL effect, heritability and incidence of categories) were simulated in our study. Daughter design with multiple families was applied, and the size of segregating population is 500. The results showed that the threshold model has a great advantage in parameters estimation and power of QTL mapping, and has nice efficiency and accuracy for discrete traits. In addition, the accuracy and power of QTL mapping depended on the effect of putative quantitative trait loci, the value of heritability and incidence directly. With the increase of QTL effect, heritability and incidence of categories, the accuracy and power of QTL mapping improved correspondingly.


Discrete Traits;Threshold Models;QTL Mapping;Maximum Likelihood


  1. Bonney, G. E. 1986. Regressive logistic models for familial disease and other binary traits. Biometrics 42:611-625.
  2. Darvasi, A. and M. Soller. 1997. A simple method to calculate resolving power and confidence interval of QTL map locations. Behav. Genet. 27:125-132.
  3. Feingold, E. 2002. Regression-based quantitative trait locus mapping in the 21st century. Am. J. Hum. Genet. 71:217-222.
  4. Haley, C. S. and Knott, S. A. 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315-324.
  5. Kim, Tae-Hun, Bong-Hwan Choi, Du-Hak Yoon, Eung-woo Park, Jin-Tae Jeon, Jae-Young Han, Sung-Jong Oh and Il-Cheong-Cheong. 2004. Identification of Quantitative Trait Loci (QTL) Affecting Teat Number in Pigs. Asian-Aust. J. Anim. Sci. 17(9):1210-1213.
  6. Wright, S. 1934. An analysis of variability in number of digits in an inbred strain of guinea pigs. Genetics 19:506-536.
  7. Xu, S. and W. R. Atchley. 1996. Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143:1417-1424.
  8. Zhang, Q., D. Biochard and I. Hoeschele. 1998. Mapping quantitative trait loci for milk production and health of dairy cattle in a large outbreed pedigree. Genet. 149:1959-1973.
  9. Chen, W. M., K. W. Broman and K. Y. Liang. 2004. Quantitative trait linkage analysis by generalized estimating equations: Unification of variance components and Haseman-Elston Regression. Genetic Epidemiology 26:265-272.
  10. Kadarmideen, H. N. and R. Thompson. 2000. Linear and threshold model genetic parameters for disease, fertility and milk production in dairy cattle. Anim. Sci. 71:411-419.
  11. Zeng, Z. B. 1994. Precision mapping of quantitative trait loci. Genet. 136:1457-1468.
  12. Falconer, D. S. 1996. Introduction to Quantitative Genetics (4rd Ed.). Longman, England.
  13. Gianola, D. 1982. Theory and analysis of threshold characters. J. Anim. Sci. 56:1079-1096.
  14. Lee, H. K., S. S. Lee, T. H. Kim, G. J. Jeon, H. W. Jung, Y. S. Shin, J. Y. Han, B. H. Choi and I. C. Cheong. 2003. Detection of imprinted quantitative trait loci (QTL) for growth traits in pigs. Asian-Aust. J. Anim. Sci. 16(8):1087-1092.
  15. Yi, N. and S. Xu. 1999. A random model approach to mapping quantitative trait loci for complex binary traits in outbred populations. Genet. 153:1029-1040.
  16. Grignola, F. E., I. Hoeschele and B. Tier. 1996. Mapping quantitative trait loci in outcross population via Residual Maximum Likelihood. I. Methodology. Genet. Sel. Evol. 28:479-490.
  17. Liu, Y., G. B. Jansen and C. Y. Lin. 2004. Quantitative trait loci mapping for dairy cattle production traits using a maximum likelihood method. J. Dairy Sci. 87:491-500.
  18. Weller, Joel Ira. 2001. Quantitative trait loci analysis in animals.UK, CABI.