The presently disclosed subject matter provides methods for improving the efficacy ofa plant breeding program aimed at altering phenotypic traits for which associations withgenetic markers can be established. Genome-wide genetic values of individuals arecomputed based on the individuals marker genotypes and the associations establishedbetween genetic markers and phenotypic traits. Individuals and breeding schemesare then selected based both on the individuals genome-wide genetic valueand on the distributions of these genetic values for the potential progeniesderived through the breeding schemes under evaluation. The presently disclosedsubject matter also provides systems and computer program products for performingthe disclosed methods as well as plants selected, provided, or produced by anyof the methods herein and transgenic plants created by any of the methods herein.
