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An investigation into the genetic basis of variation in hypoxia tolerance in Atlantic salmon Lin, Xiang


Episodes of hypoxia are becoming more common along the British Columbia (BC) coast especially in the late summer. When dissolved oxygen drops below optimum levels, fish survival, growth and reproduction are affected; moreover, hypoxia can be lethal to fish, resulting in economic losses to salmon farmers. As a first step towards addressing this challenge for BC salmon farmers, the objectives of this study were to characterize variation in hypoxia tolerance in Atlantic salmon (Salmo salar) under culture conditions and identify the genetic basis of this variation in the strains of salmon used by the aquaculture producer Marine Harvest Canada. Using time-to-loss-of-equilibrium (LOE) following exposure to acute hypoxia (2.1 mg/L) as an index of hypoxia tolerance, I show that there are significant differences in hypoxia tolerance within and between the strains of Atlantic salmon examined. For adults in seawater, time-to-LOE at 2.1 mg/L DO ranged from 4.6 min to 126.9 min, and the McConnell strain had better hypoxia tolerance than the Mowi strain. A similar pattern was observed for smolts in freshwater, with time-to-LOE ranging from 4.5 min before 2.1 mg/L DO was reached to 355.4 min at 2.1 mg/L DO. Genotyping-by-sequencing (GBS) was used to identify single-nucleotide polymorphism (SNP) markers in these strains for use in a genome-wide association study (GWAS). GWAS in adult fish in seawater revealed two SNPs associated with hypoxia tolerance using genome-wide FDR correction, and six SNPs associated with hypoxia tolerance using chromosome-wide FDR correction. In contrast, GWAS in smolts in freshwater identified one SNP using genome-wide FDR correction and one SNP using chromosome-wide FDR correction. There was no overlap in the SNPs identified as associated with hypoxia tolerance at these two life stages. In addition, I identified four significant SNPs associated with body mass in adults with chromosome-wide FDR correction and two SNPs associated with body mass with genome-wide FDR correction and fifty-eight SNPs associated with body mass with chromosome-wide FDR correction. These findings provide promise for follow-up work on SNP markers that could potentially be used for marker-assisted selection to improve hypoxia tolerance and growth in Atlantic salmon.

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