Examination of the genetic basis of the timing of the return migration of Atlantic salmon (Salmo salar) to fresh water from the sea, a trait of economic and conservation interest, was carried out using a genome-wide association study. We examined genotype data of 52 731 single nucleotide polymorphic (SNP) markers from 73 early and 49 late running two-sea-winter salmon from five rivers in eastern Scotland. A single region of the Atlantic salmon chromosome Ssa09 was identified, containing nine SNP markers significantly associated with run timing, a region previously linked to variation in sea age at maturity. Validation of the markers in a group of 233 one- and two-sea-winter fish, including adults from a novel river, again showed significant associations between the trait and the Ssa09 region, explaining ∼24% of the trait variance. The SNP loci identified provide the ability to examine trait variation in populations of Atlantic salmon and so help facilitate conservation management of the differing run timing phenotypes.
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)