Effect of the Accuracy of an Estimated QTL Effect on Response to Marker-Assisted Selection

The effect of the accuracy of estimated QTL effects on relative efficiency of marker-assisted selection (MAS) to non-MAS was investigated in a simulation study in a single trait selection scheme under variable heritability, different QTL effect and different initial QTL allele frequencies. The results showed that the probability of realized MAS response being less than expected response increased with higher standard error associated with an estimated QTL effect. This probability was significantly higher when a high standard error was associated with large QTL effects in lower QTL allele frequencies and/or lower heritability. The MAS responses could be equal or even less than non-MAS when the QTL variance from an inaccurate QTL effect constitutes a considerable proportion of overall genetic variance. This study showed that incorporating prior information about the QTL in a Bayesian approach can effectively remedy the problem of over prediction of MAS response.