Transcriptome analysis of possible genetic-level defects in the use of large-sized Chinese mitten crab ( Eriocheir sinensis ) parents for breeding

The breeding of Chinese mitten crabs (Eriocheir sinensis) commonly relies on large-sized broodstock; however, the genetic advantages and potential risks of this practice remain insufficiently evaluated. To investigate possible molecular deficiencies associated with large-sized parents, we conducted a comprehensive transcriptomic analysis during the breeding phase, focusing on offspring at key developmental stages (fertilized eggs and megalopae) and reproductive tissues of parents of different sizes (testes and accessory glands in males, ovaries in females). Our results revealed significant downregulation of pathways related to chitin synthesis and moulting cycles in offspring derived from large broodstock, with key genes including CDA1, Mco1, and FIBCD1. In addition, genes involved in sensory perception and neural development, such as CHST11, Celsr3, and EphA5, were consistently downregulated in the reproductive tissues of large-sized parents. In male accessory glands, large broodstock further exhibited reduced expression of genes associated with chromosome stability, including Hhex and PAX5. Enzyme activity assays (chitinase, carbonic anhydrase, acetylcholinesterase, and peroxidase) corroborated the transcriptomic patterns. Overall, our findings suggest that large-sized broodstock may carry latent genetic deficiencies affecting moulting, growth, neural function, and reproductive performance. This study provides a theoretical foundation for optimizing broodstock selection and advancing genetic breeding strategies in E. sinensis.