Understanding the molecular implications of in vivo ageing in pikeperch eggs via transcriptomic profiling

Egg quality unpredictability remains a significant challenge in aquaculture, limiting reproductive success and production efficiency. Identifying reliable molecular markers of egg quality is therefore essential for optimizing hatchery protocols and selective breeding strategies. Building upon our previous study that used proteomics to investigate early in vivo post-ovulatory ageing in pikeperch (Sander lucioperca), we employed a complementary transcriptomic approach to further elucidate molecular mechanisms underlying egg quality decline. The in vivo ageing model, enabled by commercially applied species-specific suture technique that prevents spontaneous egg release, provides a controlled and biologically relevant framework for identifying early-stage molecular biomarkers of egg developmental competence. Although eggs retained for 5 h post-ovulation (hPO) exhibited no visible deterioration, they showed significantly reduced fertilization and hatching success compared to eggs collected at 1 hPO. Transcriptomic profiling revealed 202 differentially expressed transcripts, implicating processes such as RNA metabolism, mRNA decay, cytoskeletal organization, and cell cycle regulation. Several hub genes (ago2, ep300, kmt2c) were identified as potential key regulators of egg competence, and ivns1abp and setdb1 emerged as promising candidate conserved markers of egg quality across species. This study advances our previous findings by revealing that transcriptomic changes, rather than proteomic alterations, are early and sensitive indicators of post-ovulatory ageing. Together, these results offer valuable insights for developing transcriptome-based biomarkers to improve broodstock management and reproductive outcomes in aquaculture.