Breeding values for identified quantitative trait loci under selection

The use of an identified quantitative trait locus (QTL) in selection requires the integration of breeding values (BV) for the known QTL with estimates of polygenic BV. For a QTL with two alleles, BV for the QTL are traditionally based on the allele substitution effect, alpha = a + d(q - p), where a and d are additive and dominance effects, and p and q are gene frequencies in the current generation. It is: shown here that to maximize single generation response, BV for a QTL with dominance must be derived based on gene frequencies among selected mates rather than frequencies in the current (unselected) generation. Because selection affects gene frequencies that in turn affect optimal BV for the QTL, gene substitution effects must be derived numerically. Response from selection on optimized versus standard BV for the QTL was evaluated for a range of parameters. Benefits of optimal selection were greatest for intermediate gene frequency and increased with a magnitude of additive and dominance effects up to 9 %. Extra response was negligible for gene frequencies less than 0.05 or greater than 0.85. In conclusion, strategies for marker-assisted selection that aim to maximize short-term response must account for the effects of dominance and changes in gene frequency at the QTL on performance of future progeny. (C) Inra/Elsevier, Paris.