Abstract: This invention relates to a method for improving the efficacy of a plant breeding program by selectively altering the average of a quantitative phenotypic trait in a plant population. The method employs statistical models to predict the association of genetic markers with a desired phenotypic trait. These models allow the association to be extrapolated to the progeny of the plants tested as well as plants in other families within the breeding population. After the statistical association has been determined, the genetic markers which associate with quantitative trait loci can be used to screen for plants with the desired genetic markers to use as progenitors of an F1 seed population. Alternatively, after the alleles which associate with a QTL have been identified, the coding sequences of at least one of the alleles can be cloned and introduced into a plant to create a transgenic plant line.