Evaluation of Reciprocal Cross Design on Detection and Characterization of Mendelian QTL in $F_2$ Outbred Populations

  • Received : 2007.03.12
  • Accepted : 2007.06.10
  • Published : 2007.11.01


A simulation study was conducted to evaluate the effect of reciprocal cross on the detection and characterization of Mendelian QTL in $F_2$ QTL swine populations. Data were simulated under two different mating designs. In the one-way cross design, six $F_0$ grand sires of one breed and 30 $F_0$ grand dams of another breed generated 10 $F_1$ offspring per dam. Sixteen $F_1$ sires and 64 $F_1$ dams were randomly chosen to produce a total of 640 $F_2$ offspring. In the reciprocal design, three $F_0$ grand sires of A breed and 15 $F_0$ grand dams of B breed were mated to generate 10 $F_1$ offspring per dam. Eight $F_1$ sires and 32 $F_1$ dams were randomly chosen to produce 10 $F_2$ offspring per $F_1$ dam, for a total of 320 $F_2$ offspring. Another mating set comprised three $F_0$ grand sires of B breed and 15 $F_0$ grand dams of A breed to produce the same number of $F_1$ and $F_2$ offspring. A chromosome of 100 cM was simulated with large, medium or small QTL with fixed, similar, or different allele frequencies in parental breeds. Tests between Mendelian models allowed QTL to be characterized as fixed (LC QTL), or segregating at similar (HS QTL) or different (CB QTL) frequencies in parental breeds. When alternate breed alleles segregated in parental breeds, a greater proportion of QTL were classified as CB QTL and estimates of QTL effects for the CB QTL were more unbiased and precise in the reciprocal cross than in the one-way cross. This result suggests that reciprocal cross design allows better characterization of Mendelian QTL in terms of allele frequencies in parental breeds.


Supported by : Korea Rural Development Administration


  1. Haley, C. S., S. A. Knott and J.-M. Elsen. 1994. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genet. 136:1195-1207.
  2. Thallman, R. M., J. O. Sanders and J. F. Taylor. 1992. Non-Mendelian genetic effects in reciprocal cross $Brahman{\times}Simmental$ $F_1$ calves produced by embryo transfer. Beef Cattle Research in Texas, PR-5053:8-14. Tex. Agri. Exp. Sta., College Station.
  3. Yang, S., Z. Zhu and K. Li. 2005. Potential of the quantitative trait loci mapping using crossbred population. Asian-Aust. J. Anim. Sci. 18:1675-1683.
  4. Liu, G., D. G. J. Jennen, E. Tholen, H. Juengst, T. Kleinwachter, M. Holker, D. Tesfaye, G. Un, H-J. Schreinemachers, E. Murani, S. Ponsuksili, J. J. Kim, K. Schellander and K. Wimmers. 2007. Identification of quantitative trait loci in a Duroc-Pietrain population. Anim. Genet. 38:241-252.
  5. Quintanilla, R., O. Demeure, J. P. Bidanel, D. Milan, N. Iannuccelli, Y. Amigues, J. Gruand, C. Renard, C. Chevalet and M. Bonneau. 2003. Detection of quantitative trait loci for fat androstenone levels in pigs. J. Anim. Sci. 81:385-394.
  6. Kim, T. H., B. H. Choi, H. K. Lee, H. S. Park, H. Y. Lee, D. H. Yoon, J. W. Lee, G. J. Jeon, I. C. Cheong, S. J. Oh and J. Y. Han. 2005b. Identification of quantitative traits loci (QTL) affecting growth traits in pigs. Asian-Aust. J. Anim. Sci. 18:1524-1528.
  7. Kim, E. H., B. H. Choi, K. S. Kim, C. K. Lee, B. W. Cho, T.-H. Kim and J.-J. Kim. 2007. Detection of Mendelian and parentof-origin quantitative trait loci in a cross between Korean Native Pig and Landrace I. growth and body composition traits. Asian-Aust. J. Anim. Sci. 20:669-676.
  8. Knott, S. A., J. M. Elsen and C. S. Haley. 1996. Methods for multi-marker mapping of quantitative trait loci in half-sib populations. Theoretical Applied Genetics 93:71-80.
  9. Alfonso, L. and C. S. Haley. 1998. Power of different $F_2$ schemes for QTL detection in livestock. Anim. Sci. 66:1-8.
  10. Bidanel, J. P. and M. Rothschild. 2002. Current status of quantitative trait locus mapping in pigs. Pig News and Information 23(2):39N-53N.
  11. De Koning, D. J., H. Bovenhuis and J. A. M. van Arendonk. 2002. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genet. 161:931-938.
  12. Choi, B. H., J. S. Lee, G. W. Jang, H. Y. Lee, J. W. Lee, K. T. Lee, H. Y. Chung, H. S. Park, S. J. Oh, S. S. Sun, K. H. Myung, I. C. Cheong and T. H. Kim. 2006. Mapping of the porcine Calpastatin gene and association study of its variance with economic traits in pigs. Asian-Aust. J. Anim. Sci. 19:1085-1089.
  13. De Koning, D. J., A. P. Rattink, B. Harlizius, J. A. M. van Arendonk, E. W. Brascamp and M. A. M. Groenen. 2001. Detection and characterization of quantitative trait loci for meat quality traits in pigs. J. Anim. Sci. 79:2812-2819.
  14. Rohrer, G. A., R. M. Thallman, S. Shackelford, T. Wheeler and M. Koohmaraie. 2006. A genome scan for loci affecting pork quality in a Duroc-Landrace F2 population. Anim. Genet. 37:17-27.
  15. Kim, J.-J., H. Zhao, H. Thomsen, M. F. Rothschild and J. C. M. Dekkers. 2005a. Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genet. Res. 85:235-248.