Expression dynamics and promoter regulation of Caspase 6 and Caspase 7 during embryogenesis of hybrid crucian carp (Carassius auratus) × common carp (Cyprinus carpio)

Distant hybridization is an important means of aquaculture breeding, which can cultivate new varieties with excellent traits and increase the output and benefits of aquaculture. However, the early embryo survival rate of the hybrid offspring is significantly lower, which limits its application. Caspase 6 and Caspase 7 are key genes in the apoptotic pathway and play a crucial role in embryonic development. This study takes red crucian carp (RCC), common carp (CC) and their hybrid offspring as the research objects to explore the genomic characteristics of Caspase 6 and Caspase 7 and their expression patterns during the early embryonic development process. The results indicated that Caspase 6 localized to 2 chromosomes in both RCC and CC genomes, while Caspase 7 had a more complex distribution. Phylogenetic tree analysis indicates that homologous genes on different chromosomes cluster together, suggesting that their multiple copies of homologous genes have the same origin. Caspase 6 and Caspase 7 exhibited distinct stage-specific expression patterns in hybrid crucian carp F 1 embryos and were highly expressed during critical embryonic development periods such as the blastocyst and long pec. Allele-specific expression analysis revealed patrilineal (CC) bias in F 1 embryos. Furthermore, the promoter sequences of these two genes are not conserved, and the promoter activity of RCC is higher. This might be due to other factors (such as DNA methylation, miRNAs) causing gene expression bias towards the father in hybrid crucian carp. These findings provide new ideas for revealing the relationship between the expression of apoptotic genes in hybrid crucian carp and the quality of early embryos, laying a theoretical foundation for fish genetic breeding. • The expression patterns of Caspase 6 and Caspase 7 during embryonic development were examined. • The expression of Caspase 6 and Caspase 7 genes in hybrid embryos shows a paternal bias. • The promoter sequences are not conserved, with red crucian carp exhibiting higher activity.