Expression of Hox genes in embryogenesis of crucian carp (Carassius carassius) × common carp (Cyprinus carpio) hybrid

Distant hybridization has been widely applied in fish breeding. Unfortunately, hybrid offspring often exhibit deformities and mortality during embryonic development. It has been demonstrated that the hybrid of the crucian carp (Carassius carassius) × common carp (Cyprinus carpio) can pass through reproductive isolation and generate fertile offspring. In the present study, we analyzed the transcriptomic changes during the embryonic developmental stages in red crucian carp (HJ), Koi carp (KOC) and the hybrid F₁. In addition, the expression of Hox genes in the three fishes was evaluated. The transcriptome expression analysis revealed that the greatest number of differentially expressed genes during the gastrula stage (GR) period was found among HJ, F₁, and KOC. Specifically, there were 3316 differentially expressed genes between KOC and F₁, 6027 differentially expressed genes between HJ and F₁, and 1232 differentially expressed genes between KOC and HJ. The identification of cis- and trans-regulatory patterns indicated that most genes subject to cis- and/or trans- were assigned to cis-trans compensating patterns, suggesting a complementary regulatory interaction between the subgenomes. The Hox gene expression comparison results indicated that the genes were low expressed in the GR stage and increased following somite formation. Although gene expression changes were found comparing the F₁ to its parents, the trend of expression changes is consistent in the three fishes. The knowledge about the transcriptomic changes and regulations in hybrids would aid to understand the interaction of subgenomes during embryonic development.