Genetics Selection Evolution 2009, 41:38 http://www.gsejournal.org/content/41/1/38 only the markers in closest association with QTL (as in BayesB). Hence, fitting population-specific markers may be of more importance, since QTL effects are likely to be attributed to a broader distribution of markers. In previous stochastic simulation or deterministic studies of introgression programs targeting a major QTL, donor and recipient lines are often assumed to be unrelated and fixed for alternative target QTL alleles [1,15,16]. For live- stock and farmed fish, these assumptions are usually unre- alistic, and provide idealized conditions for the introgression programs. In the current study, the donor and recipient lines were assumed to be only partially dif- ferentiated, and the target QTL was chosen among loci that happened to be segregating only within the donor line (since this would make introgression necessary). Hence, introgression of the major QTL would not be guar- anteed by crossing the recipient line with a small sub-sam- ple of individuals from the donor line, and one would rarely have markers in perfect LD with the major QTL. However, some simplified assumptions were made, i.e., the assumption of no pleiotropy, implying zero genetic correlation (before selection) between disease resistance and the production trait (e.g., growth). The latter is not necessarily unrealistic, but the assumption of complete absence of pleiotropic effects on all loci is most likely over-simplified. Actually, numerous pleiotropic effects in both directions (favourable/unfavourable) may underlie a genetic correlation close to zero. However, under the current assumption, different QTL for the two traits will often be closely linked, which will have an effect that resembles pleiotropic QTL. The practical consequences of this assumption are thus likely to be limited. In our view, the current method of simulation and (GBLUP) analysis is rather realistic and conservative with respect to the pros- pects for introgression schemes in livestock and farmed fish populations. Conclusion There were substantial differences between introgression programs using classical and genomic selection, with the first being generally inferior with respect to both genetic gain and the ability to preserve the target QTL. Combining genomic selection with gene-assisted selection for the tar- get QTL acted as an extra precaution against loss of the tar- get QTL and gave additional genetic gain for disease resistance. However, the effect on total merit index was limited compared with genomic selection without specific knowledge of the target QTL. Competing interests The authors declare that they have no competing interests. Authors' contributions JØ carried out the computer simulations and drafted the manuscript. MHY participated in software programming. 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