Bread wheat, a staple crop, is characterized by its evolution as an allopolyploid from three species of wild wheat. Therefore, bread wheat has three gene sets (genome) within a single cell. The bread wheat genome, being an allopolyploid, is not only complex but is also huge, which is why its genome analysis has been delayed compared to other crops. In recent years, the technological revolution in deciphering the DNA base sequence has resulted in the accumulation of genome information. Making use of such information, we are studying how bread wheat utilizes the three gene sets to build a gene control network. Applying this knowledge to molecular breeding, we address the issues of strengthening environmental adaptability, improving the quality of whear flour and its functional ingredients, and increasing yield through modification of ear shape and grass type.