The practice of synthesizing allohexaploid wheat using tetraploid wheat ancestor and the diploid Ae. tauschii has been widely used in wheat hybridization and breeding. In addition to its high genetic diversity inherited from wild ancestors, synthetic wheat is also free from reproductive isolation with cultivated wheat and has great potential for yield and stress tolerance improvement. How does hybridization and polyploidization confer adaptive advantage? Our previous results indicate that non-additive expression patterns might be involved in the process. Nevertheless, the specific regulatory basis of non-additive expression has yet to be clarified. Through integrating allele specific analysis on gene expression levels and chromatin accessibility, this study aims at identifying the cis-regulatory elements and trans-regulatory factors giving rise to non-additive expression. Moreover, this study plans to conduct these analyses in different tissues, developmental stages and stress conditions and using different parental combinations. This allows to verify the “expression complementation” hypothesis in explaining hybrid vigor and enables associating parental variation and regulatory mechanisms with specific agronomic traits in synthetic wheat. The findings of this study will fill important theoretical gap for synthetic wheat breeding and provide invaluable resource for targeted and precise breeding in common wheat.