Genetics Selection Evolution 2009, 41:38 http://www.gsejournal.org/content/41/1/38 Background In domesticated populations, specific traits of interest may be improved through introgression of genes from a donor line favourable with respect to a trait of interest (e.g., a wild population resistant to a specific disease). However, the donor line is often inferior with respect to other traits included in the breeding objective of the recip- ient line (e.g., production), which hampers crossbreeding. Introgression schemes may be carried out through a back- cross breeding program aimed at introgressing a single gene from the donor line into the genomic background of a recipient line, where molecular markers can be used to assess the presence of the introgressed gene [1]. Successful marker-assisted introgression programs have been con- ducted, using markers linked to known QTL positions [2,3]. An alternative strategy to traditional introgression schemes is to combine introgression and QTL detection into a single step [4]. An even simpler approach is to com- bine introgression with a genomic selection program [5], where individuals are selected based on estimated marker effects distributed over the entire genome. Hence, within- strain selection for desired alleles from both lines may be initiated directly on the F1 crossbreds avoiding loss of time on initial QTL detection studies. In a previous simulation study [6], genetic material was introgressed from a donor line (inferior with respect to production, but superior with respect to disease resist- ance), into a recipient line (superior with respect to pro- duction, but inferior with respect to disease resistance), assuming that both traits were controlled by many QTL. The results indicated that, compared with pure breeding, an introgression program using genomic selection pro- duces a more resistant and economically competitive crossbred population within relatively few generations [3- 5]. Therefore, introgression combined with genomic selection was suggested as a tool for introgressing genetic material from inferior donor lines into recipient popula- tions. The current study is an extension of the previous study, taking a major QTL into consideration. Typical introgression programs, aim at introgressing one or more alleles of interest from the donor line, while simultaneously reducing the amount of donor DNA to a minimum. Here, genomic selection will not necessarily reduce the amount of donor DNA, but should lead to an increase of the frequency of favourable alleles, irrespective of their origin [6]. In simulated introgression schemes, Groen and Smith [7] have concluded that selection for genomic similarity to the recipient line is less efficient than selection for phenotype. In the current study, indi- viduals are selected based on total genetic value, summed over all markers (irrespective of origin). Hence, any favourable allele from the donor line may be introgressed. Introgression of major QTL alleles is therefore likely, although not assured. This strategy is particularly relevant when (major) QTL are not known prior to selection. The aim of this study was to investigate whether genomic selection methods [5] can be used to introgress a major QTL allele through a backcrossing program in a situation where both the location and the effect of the QTL alleles are unknown, and when the trait is also affected by numerous minor genes. The genomic selection schemes was compared with classical selection schemes without the use of any genomic information and schemes using genomic selection for minor QTL combined with gene- assisted selection for the major QTL. The latter alternative can be seen as a best-case scenario for introgression of spe- cific QTL alleles of interest. Methods The selection experiment was designed to use genetic resources from two partially separated populations. Gen- erally, two fish populations were simulated as in Ødegård et al. [6]. The common base population was generated and mated randomly with replacement for 10,000 generations (effective population size Ne = 1000), subsequently the base population was randomly split into two equally sized (Ne = 1000) subpopulations, which were kept sepa- rate for the following 250 generations. Finally, for 10 gen- erations, one population (recipient line) was phenotypically selected for a production trait (PT), with a heritability of 0.1, by selecting the top 10% of males and top 10% of females. The other population (donor line) was randomly selected with replacement (random 10% of the males and females). The purpose of the separation period was to generate two partially differentiated popu- lations that were at different genetic levels for important traits. A single major QTL for disease resistance (DR) was assumed to segregate only within the donor line. Ran- domly selected sires and dams from the resulting two lines were then used as parents for two lines; one purebred recipient line selected for PT only (PRL = production line) and an F1 cross in the following selection experiment over five generations (S1 to S5). Different replicates were sim- ulated separately, but the initial generation (S0) was iden- tical for all scenarios within each replicate. Selection Two selection strategies were used for generations S1 – S5: 1) Pure breeding of the recipient line for backcrossing for a breeding objective including only one production trait (PT), i.e., a production line (PRL), which represents an external commercial population included in a classical selection program for improved production, and 2) an introgression strategy by creating F1 crossbreds of recipi- ent and donor lines, followed by repeated backcrossing to the PRL, i.e., a BACKCROSS line. Backcrossing was done only to the extent that females from the PRL were superior Page 2 of 10 (page number not for citation purposes)