Genetics Selection Evolution 2009, 41:38 http://www.gsejournal.org/content/41/1/38 Table 2: Average genetic gains from generation S0 to S5 of the different selection schemes for production trait (PT), disease resistance (DR) and total merit index (TMI). Scenario Population structure Selection criteria Genetic gain PT Genetic gain DR Genetic gain TMI 1 2 PRL BACKCROSS BACKCROSS BACKCROSS PRL BACKCROSS BACKCROSS BACKCROSS CBLUP CBLUP GBLUP GasGBLUP CBLUP CBLUP GBLUP GasGBLUP 3.12 (0.10) 5.61 (0.17) 5.56 (0.19) 5.49 (0.18) 3.12 (0.10) 5.44 (0.17) 5.15 (0.19) 5.09 (0.17) -0.04 (0.07) 0.01 (0.11) 1.59 (0.13) 2.24 (0.12) -0.04 ((0.07) 0.32 (0.11) 2.14 (0.12) 2.73 (0.09) 2.78 (0.09) 5.02 (0.16) 5.69 (0.14) 5.91 (0.14) 2.78 (0.09) 4.71 (0.13) 5.48 (0.13) 5.75 (0.13) All genetic gains are measured in Background genetic standard deviations with standard errors given in parentheses PT = production trait, DR = disease resistance, EW = relative economic weight, assuming equal genetic variance for the two traits limited advantage of GasBLUP over GBLUP with respect to genetic gain in TMI (4%) can be explained by the high relative economic weight of PT. The frequencies of the favourable major QTL allele by gen- eration are shown in Figure 2 (single replicates and aver- age level). In the introgression schemes using classical selection (CBLUP), backcrossing with the PRL line was continued throughout the entire selection experiment, and average expected frequency of "neutral" donor alleles (based on pedigree) was therefore as low as 4% at genera- tion S5 (Figure 2a). Consequently, average frequency of the favourable major QTL allele also dropped from 23% at generation S0 to 4% in generation S5, and ended up as lost in 27 out of 50 replicates (Figure 2a). For the intro- gression schemes using genomic selection (GBLUP/GasG- BLUP), backcrossing with the PRL mainly occurred up to generation S2, and the expected frequency of "neutral" donor alleles in the GBLUP/GasGBLUP alternatives thus stabilized at, respectively, 15 and 16% towards the end of the selection experiment (Figure 2b and 2c). Using GBLUP, the average frequency of the favourable allele for the major QTL dropped from 23% at generation S0 to 11% at generation S2 (Figure 2b), as a result of backcross- ing with PRL. Using GasGBLUP, the frequency of the favourable major QTL allele was stable for S0 to S2 (Figure 2c). However, as a result of genomic/gene-assisted selec- tion within the crossbred population, the average fre- quency of the major QTL increased from S2 and onwards for both GBLUP and GasGBLUP (to respectively 32% and 81% in generation S5). The favourable QTL allele was never lost using GasGBLUP, but it was lost in 6 out of 50 replicates using GBLUP. gain observed for PT. Again, genomic selection increased genetic gain for TMI compared with classical selection (16 and 22% for GBLUP and GasGBLUP, respectively). Clas- sical selection led to substantial backcrossing, and the expected amount of "neutral" donor alleles was therefore as low as 5% in generation S5 (Figure 3a), and had a lim- ited effect on the frequency of the favourable major QTL, reaching an average frequency of 5% in generation S5, while being lost in 29 out of 50 replicates (Figure 3a). Compared with GBLUP, GasGBLUP selection was supe- rior with respect to genetic gain in DR (28%), slightly infe- rior with respect to genetic gain in PT (-1%) and slightly superior with respect to genetic gain in TMI (5%). Again, backcrossing with the PRL mainly occurred up to genera- tion S2 in both GBLUP and GasGBLUP selection schemes, and the expected frequency of "neutral" donor alleles sta- bilized at 17% and 18%, respectively (Figure 3b and 3c). For the GBLUP selection scheme, the frequency of the favourable major QTL allele followed the same pattern as in the scenario above (Figure 2b), although the initial drop (from S0 to S2) in the average frequency of the favourable major QTL allele was smaller (from 23 in S0 to 13% in S2), as expected through reduced backcrossing. For the GasGBLUP selection scheme (Figure 3c), the fre- quency of the favourable major QTL allele increased throughout the entire selection experiment, but most markedly after generation S2, where backcrossing had essentially ceased. The average end-frequency of the favourable major QTL allele (at S5) was 43% and 93%, for GBLUP and GasGBLUP schemes, respectively. Again, the favourable allele was never lost using GasGBLUP, but it was lost in 5 out of 50 replicates for GBLUP. Scenario 2: ratio of economic weights for PT and DR 3:2 Genetic gains (from S0 to S5) are shown in Table 2. Gen- erally, ranking of selection schemes was similar to that in Scenario 1, with the largest differences in genetic gain observed for DR, and the smaller differences in genetic Discussion The results of this study clearly show that genomic selec- tion can to a large extent identify relevant DNA segments for both traits and use this information in selection, while classical selection has a limited effect on alleles affecting Page 5 of 10 (page number not for citation purposes)