Genetics Selection Evolution 2009, 41:38 http://www.gsejournal.org/content/41/1/38 [12]. The CBLUP of DR for selection candidates was calcu- lated based on sib and pedigree data (including pheno- types back to generation S0). The GBLUP and GasGBLUP values were scaled by a factor b ( = Cov(TBV ,EBV) ) , in Var(EBV) order to make them directly comparable to CBLUP values. All breeding values and the factor b were re-estimated for each generation (the latter was based on all individuals with genomic EBV across generations). Scenarios Backcrossing schemes were conducted for the different selection criteria (using CBLUP, GBLUP and GasGBLUP). Two sets of economic weights were used; either 100% (2:1) (Scenario 1) or 50% (3:2) (Scenario 2) higher rela- tive weight on PT compared with DR (Table 1). In the crossbred population, selection was for total merit index (TMI), with the selection criteria defined as the sum of predicted breeding values for both traits, multiplied by their corresponding economic weights. For all settings, the PRL was selected for PT using only the CBLUP selec- tion criterion. Calculation of summary statistics A total of 50 replicates were produced for each scenario and selection scheme. Within each replicate, the average frequency of the favourable major QTL allele and the aver- age level of true breeding values (DR, PT and TMI) were calculated, and subsequently averaged over all 50 repli- cates. Genetic gains for PT, DR and TMI were calculated as average differences in true genetic level from generation S0 to S5. For comparison purposes, the expected fre- quency of the target QTL given no selection (but identical amounts of backcrossing) was calculated as the expected genetic contribution of the donor population (based on pedigree) multiplied with the original frequency of the favourable target allele in the donor population. Table 1: Description of the selection schemes 1 2 PRL BACKCROSS BACKCROSS BACKCROSS PRL BACKCROSS BACKCROSS BACKCROSS Results At generation S0, the average genetic differences (in back- ground genetic standard deviations) between the recipient (PRL) and the F1 crossbred populations were 2.5 and -0.4 for PT and DR, respectively (difference in DR mainly due to the major QTL). Consequently, TMI differed for the two populations. Assuming 100% higher economic weight for PT (economic weights 2:1), the average difference in TMI was 2.1 genetic standard deviations, and 1.9 genetic standard deviations, assuming 50% higher economic weight for PT (economic weights 3:2). The initial fre- quency of the favourable major QTL allele was 0% in the PRL (recipient) line and, on average, 23% in the F1 BACK- CROSS population. Scenario 1: ratio of economic weights for PT and DR 2:1 Genetic levels by generation for PT, DR and TMI are shown in Figure (1a, b and 1c, respectively) and genetic gains (from S0 to S5) are shown in Table 2. As in Ødegård et al. [6], genomic selection was in general favourable compared with classical selection. With respect to DR (the trait affected by the major QTL), there were substantial differences in genetic gain between the alternatives using classical selection (CBLUP) and those using genomic selection (GBLUP and GasGBLUP). As a result of repeated backcrossing with the PRL, no significant genetic gain for DR was achieved through CBLUP. However, substantial genetic gain was achieved when using genomic selection, both as a result of the more efficient within-line selection and as a result of less sustained backcrossing with the PRL. As expected, genetic gain in DR was the highest with Gas- GBLUP (increase by 40%, compared with GBLUP). The selection methods differed much less with respect to genetic gain for PT, i.e., selection for improved PT was about as efficient using genomic or classical selection (- 1% and -2% for GBLUP and GasGBLUP, respectively) despite more backcrossing with PRL under classical selec- tion. Consequently, genetic gain in TMI was higher for genomic than for classical selection (13 and 18% increase for GBLUP and GasGBLUP, respectively). The relatively CBLUP CBLUP GBLUP GasGBLUP CBLUP CBLUP GBLUP GasGBLUP 1 2 2 2 1 3 3 3 0 1 1 1 0 2 2 2 Scenario Population structure Selection criteria EW PT EW DR PT = production trait, DR = disease resistance, EW = relative economic weight, assuming equal genetic variance for the two traits Page 4 of 10 (page number not for citation purposes)