The superior performance of hybrids to parents, termed heterosis, has been widely utilized in animal and plant breeding programs, but the molecular mechanism underlying heterosis remains an enigma. RNA-Seq provides a novel way to investigate heterosis at the transcriptome-wide level, because gene expression functions as an intermediate phenotype that contributes to observable traits. Here we compared embryonic gene expression between chicken hybrids and their inbred parental lines to identify inheritance patterns of gene expression. Inbred Fayoumi and Leghorn were crossed reciprocally to obtain F1 fertile eggs. RNA-Seq was carried out using 24 brain and liver samples taken from day 12 embryos, and the differentially expressed (DE) genes were identified by pairwise comparison among the hybrids, parental lines, and mid-parent expression values. Our results indicated the expression levels of the majority of the genes in the F1 cross are not significantly different from the mid-parental values, suggesting additivity as the predominant gene expression pattern in the F1. The second and third prevalent gene expression patterns are dominance and over-dominance. Additionally, we found only 7–20% of the DE genes exhibit allele-specific expression in the F1, suggesting that trans regulation is the main driver for differential gene expression and thus contributes to heterosis effect in the F1 crosses.