Transcriptomic comparison between wild-caught and domesticated black tiger shrimp (Penaeus monodon) in early and late-vitellogenic broodstock females

Domesticated Penaeus monodon broodstock females (DF) are currently dominating the shrimp industry in Vietnam and globally. However, the downgraded quality of DF compromises the sustainability of P. monodon production. Compared with DF, wild-caught broodstock females (WF) exhibit superior survival rate, offspring quality, and anti-pathogen capability, attracting interest from the seed production sector. To understand their reproductive biology and maturation at a molecular level, we conducted a comprehensive transcriptomic analysis of P. monodon broodstock females from domestication and wild sources. We performed a comparative analysis for ovaries, hepatopancreas, and eyestalks at previtellogenesis (stage I) and late cortical rod stage (stage IV). The analysis generated 13,801 differentially expressed genes (DEGs), of which the number of downregulated genes exceeded that of upregulated genes at stage I. Similarly, the number of downregulated genes surpassed the number of upregulated genes in stage IV, apart from hepatopancreas, where the number of upregulated genes increased compared to the downregulated ones. This expression pattern suggests that the number of DEGs depends on the vitellogenic stages and tissues where they are expressed. A comparative DEG profiling study of WF and DF highlights the key genes that are likely to enhance the reproductive traits, classified into signaling and transporting in stage I, anti-pathogens, molting and reproduction genes in stage IV, deepening our understanding of the molecular events during vitellogenic stages. Our study provides candidate genes for genetic selection and/or gene manipulation to improve the reproductive traits in the domesticated P. monodon broodstock females. • The number of DGEs, a crucial aspect of our study, varies significantly depending on the stage where they are expressed. • Wild-caught fermales (WF) had more genes for transport and tolerance but fewer signaling genes than domesticated ones (DF). • WF upregulated anti-pathogen genes but downregulated crustacean hyperglycemia hormone genes in the late cortical rod stage. • Providing a list of reproduction-related genes, with expression profiles, has been linked to enhanced reproduction in WF.