Molecular dominance investigation for large-sized parents of Chinese Mitten Crab ( Eriocheir sinensis ) based on ovarian transcriptome

Abstract Background: Germplasm degradation is one of the important issues for the healthy development of Chinese Mitten Crab (Eriocheir sinensis) industry. Nowadays, nursery units and crab farmers have realized the seedling superiority of large-sized parents (≥200g male, ≥150g female), but the underlying molecular mechanisms remain unclear. Here we investigated the advantage of breeding with large-sized parents based on ovarian transcriptome.Results: RNA isolation and transcriptome sequencing were performed using ovarian tissue obtained from three large-sized female E. sinensis and three medium-sized female E. sinensis. The differentially expressed genes (DEGs) were investigated between two groups, followed by the exploration of common DEGs (co-DEGs) among the DEGs in the current study and published genes for growth, reproduction, and immune response pathways. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate all co-DEGs. Finally, a pathway enrichment analysis was performed to investigate the potential pathways associated with the validated co-DEGs. A total of 5,307 up-regulated genes and 3,465 down-regulated genes were investigated between the two groups, of which 43 co-DEGs were explored when all the DEGs in the current study were integrated with 338 genes in 15 reproductive, immune, and growth pathways. A total of nine co-DEGs, including TRINITY_DN13931_c0_g1, TRINITY_DN1908_c0_g2, and TRINITY_DN6686_c0_g1, were enrolled for further study after qRT-PCR validation. These validated co-DEGs were mainly enriched in pathways such as apoptosis, insulin signaling, and mTOR signaling. Conclusion: Our original work might lay an important molecular foundation for further exploring the advantages of using large-sized parents for E. sinensis breeding in the future. Based on the comparative analysis of gene expression, the advantages of breeding large-sized female E. sinensis parents at the molecular level, such as growth, reproduction, and immunity, were analyzed for the first time. The apoptosis pathways, insulin signaling pathways, and mTOR signaling pathway might be involved in the advantage of breeding large-sized female E. sinensis parents.