The subgenomes of an allopolyploid crop will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can therefore be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. With the availability of affordable genotyping and a reference genome to locate markers, breeders of allopolyploids now have the opportunity to manipulate subgenomes independently and fix beneficial interactions across subgenomes. I present a statistical framework for partitioning genetic variance to individual subgenomes of an allopolyploid, predicting breeding values for each subgenome, and evaluating the magnitude of homeologous epistasis. I also present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and to determine their importance within a population. I search for genome-wide patterns indicative of homeoallelic subfunctionalization in a winter wheat breeding population by anchoring homeologous marker sets to the IWGSC RefSeq v1.0 sequence. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern. Using genomic prediction accuracy to evaluate importance of marker interactions, I show that homeologous interactions explain a significant portion of the non-additive genetic signal. Allopolyploids have traditionally been treated as diploids in breeding programs because they undergo disomic inheritance. With modern DNA marker technology and ever increasing computational power, I provide a new framework for breeders of allopolyploid crops to characterize the genetic architecture of existing populations, determine breeding goals, and develop new strategies for selection of additive effects and homeologous epistasis in these ancient immortal hybrids.