Abstract
Optimization of aquaculture output requires a thorough assessment of growth and reproductive performance in farmed fish and shellfish, as a clear understanding of the reproductive trait regulation is essential for selective breeding programs. This review aims to provide a comprehensive synthesis of gonadogenesis and its regulatory mechanisms in farmed bivalves, while highlighting key knowledge gaps that remain to be addressed. In the first section, we present an overview of germ cell and associated somatic cell development and interaction, review sex determination/differentiation, and describe the reproductive modes and gametogenic processes observed in these sessile organisms following sexual maturation. Secondly, we outline current knowledge of the mechanistic regulatory processes controlling these traits, including the roles of key genes, epigenetic control, and transcriptional regulators. Furthermore, we integrate recent molecular, cellular, and physiological findings, while critically highlighting key points where knowledge remains limited or incomplete, and where further validation and investigation are required. Finally, we summarize recent advances concerning the effect of external factors and elucidate how environmental factors such as water temperature, food availability, and chemical contaminants mechanistically affect gonadogenesis. Despite advancement and significant progress driven by hatchery technologies and sophisticated research methodologies, a comprehensive understanding of the interactions between environmental and genetic factors shaping this peculiar process remains elusive. Future research incorporating multi‐omics approaches holds great promise for disentangling the genetic and regulatory architecture underlying gonadogenesis in these organisms, hence improving aquaculture production and breeding programs.