Table 1.

List of the 11 clonal doubled haploid rainbow trout and steelhead lines used in this whole-genome resequencing for SNP discovery study.

Line name	Sex	Geographic origin	Life history type	Wild or domesticated origin
Whale rock male	YY male	Central California Coast	Landlocked steelhead	Wild
Whale rock female	XX female	Central California Coast	Landlocked steelhead	Wild
Arlee	YY male	Northern California	Resident	Domesticated
Hot creek	YY male	Northern California	Resident	Domesticated
Oregon State University	XX female	Northern California	Resident	Domesticated
Golden	YY male	Northern California	Resident	Domesticated
Skookumchuck	YY male	Chehalis River*	Winter Steelhead	Semi-wild
Klamath	YY male	Williamson River†	Possibly resident	Wild
Skamania	XX male‡	Lower Columbia River*	Summer steelhead	Semi-wild
Touchet	YY male	Walla Walla River*	Inland summer steelhead	Wild
Clearwater	YY male	Snake River#	Inland summer steelhead	Semi-wild
Swanson@	YY male	Kenai Peninsula, Alaska	Resident	Semi-domesticated@

Information is also provided on the Swanson line, which is the source of the current rainbow trout reference genome.

^*Washington tributary.

^†Oregon tributary.

^‡This line is phenotypically a male, but it lacking the sdy gene.

^#Idaho tributary.

^@The line was established from a fish that was in the second generation of the hatchery program, or two generations removed from the wild origin of this population.