Illustration of the evolution of a QTL.

A Starting from an ancestral point, mutations in a particular gene accumulate (numbered black bars, representing mutations in B), resulting in new alleles. At some point, a mutation arises which improves a trait, resulting in a donor allele for a QTL (dark/red), distinguishing it from known recipient alleles (light/blue); typically the status of many alleles is unknown (white). C Each mutation (1–21) is a potential marker, and all are found in the same gene, but some are more informative than the others. Comparing the false positive and false negative rates for each mutation allows the determination of which polymorphism gives the most reliable discrimination between the donor and recipient phenotype classes.