Genomic Signatures of Domestication in Two Independently Developed Hatchery Steelhead (Oncorhynchus mykiss) Strains Propagated in Western Washington

Two hatchery strains of steelhead, a summer run and a winter run strain, were developed in the 1940s and 1950s to provide fish for harvest in recreational fisheries.  Founders for both strains were selected from early maturing fish.  Progeny were reared for a single year before release – natural populations in the region typically spend two years rearing in freshwater – and subsequent generations of broodstock were drawn from returning adults, effectively selecting parents that completed their life-cycle with a single winter of feeding and care in hatcheries.  We used restriction-site associated DNA (RAD) sequencing to discover over 20,000 polymorphic loci in 10 haploid steelhead families that represent 3 domesticated and 2 non-domesticated breeding groups.  We constructed dense linkage maps and selected a set of broadly-distributed loci to use in scanning for patterns of polymorphism that differentiate domesticated and naturally-produced populations.