Genetics and 'Omics' Technologies Review for Salmon Hatcheries

Given the current research focus on salmon genomics and transcriptomics technologies, there are several examples of hatchery deliverables. A broad-sense genomics tool that shows up repeatedly is parentage-based tagging (PBT), because of the amount of new information that can be provided for assessing hatchery performance and addressing knowledge gaps. This review has found that a breeding design (i.e. full factorial) with PBT can provide estimates of genetic and maternal effects explaining salmon traits important to hatcheries, e.g. fishery or escapement contributions. Large genetic effects can be examined further using an ‘omics’ technology to identify the specific targets increasing offspring quality, e.g. gene biomarkers. PBT is repeatedly identified as a useful tool because of the amount of new information that can be provided, especially for the adult life stage. In contrast, the newer proteomics and metabolomics technologies have fewer examples of hatchery deliverables so far. There are also potential hatchery deliverables that could be derived using environmental RNA, but these are theoretical and require further research to demonstrate feasibility. The review also identified four knowledge gaps: (1) group performance, (2) offspring quality, (3) health and condition biomarkers, and (4) hatchery-wild differences. Filling in the four knowledge gaps using ‘omics’ technologies can provide guidance on how to improve hatchery performance and assess effects on natural populations.