Genetics Selection Evolution 2009, 41:38 http://www.gsejournal.org/content/41/1/38 to females recruited from within the crossbred population based on their EBV for total merit index (TMI), i.e., females were selected among all candidates in both popu- lations, while males were selected within the crossbred population only. For generations S0 to S5, all lines were kept at a constant size of 1000 breeding candidates within each line. For the parents of S0, random selection and mating using sam- pling with replacement was applied, while, for the later generations, truncation selection based on predicted EBV was used (50 sires and 50 dams per line). The selected sires and dams were randomly mated (using sampling with replacement) to create 50 full-sib families with 20 offspring each to form selection candidates for the next generation for each line. Additionally, all 50 families within the BACKCROSS line each produced 20 offspring, which were used in sib-testing for DR. Genome structure The genome structure in this simulation was identical to that of Ødegård et al. [6], i.e., with 10 diploid 100 cM chromosomes assuming the Haldane mapping function and a Mendelian inheritance of all loci. For each chromo- some, 500 marker loci were assumed, as well as 100 QTL per trait (PT and DR). Markers and QTL loci were ran- domly spaced throughout each chromosome. Rates of mutations (per allele and meiosis for each generation) for marker and QTL alleles were 0.0001 and 0.00001, respec- tively. Mutation rates at markers were increased to ensure that most markers were segregating. All mutations gener- ated new alleles, and thus, all loci were potentially multi- allelic. The QTL allelic effects were assumed to be additive, and were sampled from a gamma distribution (shape and scale parameters of 0.40 and 0.13, respectively). Since this distribution only produces positive values, each QTL allelic effect had a 50% probability of being switched to a negative value. No pleiotropy was assumed, implying zero genetic covariance between the traits before selection. At generation t = 10,250 (10,000 + 250), QTL effects of both traits were scaled to achieve identical background genetic standard deviations (= 1.0) for both traits within the recipient line for all replicates (before selection). Scaling of QTL effects was identical for all individuals, irrespective of population. At generation t = 10,260 (10,000 + 250 + 10), ~80% of the marker loci and ~15% of the QTL were segregating within each subpopulation. Linkage disequilibrium between adjacent markers was calculated as the standardized chi- square, χ2' [8,9]. Within each base population, average calculated and expected [10] LD for adjacent markers (expectation based on actual distance) were both 0.2. At generation S0 of the selection experiment, genomes of all individuals were scanned to identify bi-allelic QTL affecting DR, where one of the alleles happened to be fixed in the recipient line, but an alternative allele existed in the donor line. The QTL displaying the largest differ- ence in allele frequencies between the lines was assumed to be a major QTL. The favourable allele (the allele absent in the recipient line) was given a genotypic value [11] of a = 2.0 (twice the background genetic standard deviation), while the genotypic value of the alternative allele was a = -2.0. Data As in the study by Ødegård et al[6]., the true breeding value of an individual was defined as the sum of QTL allelic effects for the individual across all 1000 QTL loci for each trait. Phenotypes of both traits were produced by adding normally distributed error terms, sampled from N(0, σ e2 ), to the true breeding values of each individual. Heritabilities are presented as the following: h 2 = σ a2 σ a2 +σ e2 where σ a2 is the (background) additive genetic variance (= 1.0 for both traits) within the original recipient line (not segregating for the major QTL), and σ e2 is the resid- ual variance (= 9.0 for both traits). The resulting back- ground heritability (not accounting for the major QTL) was therefore 0.10 for both PT and DR. It was assumed that all individuals within the BACKCROSS line were gen- otyped for the available 5000 marker loci. The PT was recorded on all selection candidates (1000 individuals per line and generation), while disease resistance (DR) was recorded on full-sibs of the selection candidates, using a challenge-test type of design (1000 individuals per gener- ation for the BACKCROSS line). For the PRL, only the average genetic level of DR was assumed to be available. Individuals challenge-tested for DR were not considered as selection candidates. Breeding value estimation For comparison purposes, genomic (GBLUP), gene- assisted genomic (GasGBLUP) and classical (CBLUP) EBV were produced and used as selection criteria. The GBLUP were estimated as in Ødegård et al. [6] using the BLUP esti- mation procedure of marker effects [5]. Marker by base population effects were estimated, i.e., all markers were traced back to their original populations. For GasGBLUP, the same method was used, but the effect of the major QTL was assumed known in the breeding value estima- tion. The CBLUP were estimated using classical BLUP Page 3 of 10 (page number not for citation purposes)