Advances in genome editing have enabled new potential for improving the genetics of aquaculture species. For species such as salmonids where genome editing technology is highly effective and well-established, the ability to modify new production traits is limited only by our knowledge of salmonid molecular physiology. Knowing what to edit is a serious challenge since identifying genetic mechanisms underlying key production traits can take decades of basic research.
The explosion of the field of aquaculture genomics has dramatically increased our understanding of genome structure in many species, but significant work remains to exploit this information to define how the genome functions. To help address the daunting task of characterizing genome function in rainbow trout, Oncorhynchus mykiss, major efforts are underway to integrate genome editing capabilities with modern machine learning technology to rapidly assess the impact of gene edits on fish physiology. This ongoing Decode the Salmonid Genome Project is initially focused on genetic traits associated with growth and environmental resilience in trout but also is laying the foundation for investigating other key production traits. Currently, hundreds of unique genetic lines are being examined in mass phenomics trials (i.e., growth, thermal and hypoxia tolerance) to identify high performing genetics.
The information we have gained has provided new insights into potential mechanisms of enhancing production and sustainability in this species. This knowledge is beginning to define core biological mechanisms that could form the foundation of intelligent genome design of rainbow trout as well as other commercially valuable salmonid species. Our work demonstrates the power of high-throughput genome characterization as an underlying tool for promoting a future where genome designed aquaculture species are commonplace.