In accordance with an embodiment of the invention, a system and method is provided for determining a probability of a progeny having one or more phenotypes Phj each associated with a single gene Qj. A score sip may be assigned to each allele hip at a plurality of genetic loci (i) in a haploid genome profile Hp of a parent (p). A plurality (Nj) of the alleles hkp (k=1, . . . , Nj) associated with the gene Qj may be identified. The scores sip may be mapped or indexed to gene-specific scores ŝj,kp associated with gene Qj for the plurality of (Nj) alleles hkp. A probability may be computed for altering the gene product from gene Qj in a progeny of the parent (p) to be a function of the gene-specific scores ŝj,kp.