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Using GasGBLUP, the frequency of the favourable major QTL allele was stable for S0 to S2.
The average end-frequency of the favourable major QTL allele (at S5) was 43% and 93%, for GBLUP and GasGBLUP schemes, respectively.
The initial frequency of the favourable major QTL allele was 0% in the PRL (recipient) line and, on average, 23% in the F1 BACKCROSS population.
For the GBLUP selection scheme, the frequency of the favourable major QTL allele followed the same pattern as in the scenario above, 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.
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.
Therefore, the results of this study indicate that the main advantage of GasGBLUP compared with GBLUP selection is that it acts as a precaution against the loss of the favourable major QTL allele during the early backcrossing phase.
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