Bread wheat (Triticum aestivum) is one of the most important crops worldwide. Improved knowledge of the wheat genome will facilitate marker-assisted selection that, in turn, will accelerate breeding of improved varieties, cloning of genes underlying important traits, and the transfer to wheat desirable genetic information from its wild progenitors and other related species. In addition to its indisputable agronomical importance, bread wheat represents an excellent model to study the evolution, structure, and function of allopolyploid genomes. One of the most important questions with respect to hybrid genomes is the regulation and expression of homoeologous genes in allopolyploid. We propose to sequence chromosome arm 3DS of hexaploid wheat, annotate genes and compare them to homoeologous loci on chromosomes 3A and 3B. We intend to use homoelogous gene sets to identify specific polymorphism and use this information to characterize homoeolog-specific expression of genes.