Heterosis is a powerful and valuable tool for commercial beef producers, especially cow calf operations. Despite the importance of heterosis, and its extensive genetic analysis, little understanding exists of its molecular basis. We applied RNA-Seq technology to assess transcriptome-wide allele-specific gene expression (ASGE) in the hybrid genetic background at economic traits of offspring and maternal. 120 genes of these were different expression among three individuals in common. Among these genes, we found that three genes involved in melanogenesis pathway, including MC1R, DCT and TYR. In addition six of the altered expression genes were related to arachidonic acid (AA) metabolism, such as PTGS1, PTGIS, PTGR1, ALOX12B, ALOX15B and EPHX2. We find that coat color traits could be utilized to check the analysis pipeline for heterosis studies. Results from this study indicate that the parental alleles have un-equivalent functions in the hybrid, which may have an impact on heterosis.