Developing high-performance Chinook salmon stocks for use in aquaculture: microbiome, alternative reproductive tactics and cryopreservation

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The primary objectives of the proposed research are to (1) improve broodstock production and quality via a better understanding of the gut microbiome, growth and flesh quality genetic markers and the use of male alternative reproductive tactics and (2) to create an affordable and reliable protocol to cryopreserve genes for the best lines of Chinook salmon (Oncorhynchus tshawytscha) for use in the Organic Salmon Aquaculture industry on the west coast of Canada. The broodstock and strains must therefore not only have high growth and reproductive performance, they must also have exceptional disease resistance, because theraputant use is not possible. We will address our objectives with 3 broad goals; (1) use the existing broodstock of Chinook salmon at our Industrial partner's (Yellow Island Aquaculture Ltd.; hereafter YIAL) facility to conduct a quantitative genetic based study of the gut microbiome, gut wall transcriptome and a genotype-by-sequencing (GBS) approach to detecting growth and flesh quality single nucleotide polymorphism (SNP) markers to improve broodstock performance, (2) evaluate the use of both male alternative reproductive tactics to improve broodstock production using a split-clutch in-vitro quantitative genetic breeding experiment, and (3) develop an affordable and reliable sperm cryopreservation method to store genes (genome banking) of optimal lines of salmon produced by this research and other ongoing research at our industrial partner's facility. The proposed project will not only provide solutions for the salmon aquaculture industry, it will also increase our knowledge of the genetic architecture of fitness-related traits in Chinook salmon. The proposed research will therefore provide opportunities for the academic partners to collaborate with the Canadian aquaculture industry, as well as generate applied and basic science, highly trained students and publications.******