A review of genomics application in aquaculture: status, challenges, and priorities for future direction

Aquaculture has witnessed excellent growth in recent decades, with significant potential for protein nutrition security and jobs. Genomics has significantly enhanced aquaculture technologies across various species and culture processes, improving production efficiency and profitability. With the continuous advances in next-generation sequencing technologies and bioinformatics, substantial genomic resources have been obtained for dozens of aquaculture species. These include the development of high-quality whole-genome sequences, transcriptome databases, and molecular markers, mainly single nucleotide polymorphisms (SNPs), followed by the discovery of high-density linkages and physical maps. This review presents an overview of recent advancements in aquaculture genomics, including genome sequencing and assembly, molecular breeding, genetic characterization of traits, health and biodiversity assessments, and conservation biology of fish and shellfish. The review further examines the challenges impeding the effective implementation of genomics in aquaculture research, as the full potential remains underexploited within this sector. Finally, we highlight the available opportunities, including discussing the future priorities for technologies, auspicious science, and governmental policies for realizing the fullest benefit of genomic advancement in improving the aquaculture industry. The suggestions proposed in this review will facilitate using genomic-informed data to manage valuable aquaculture resources.