Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array

Canadian Journal of Fisheries and Aquatic Sciences
By: , and 

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Abstract

Natural-origin steelhead trout (Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ∼57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean FCT = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (mean FST = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies.

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Additional publication details

Publication type Article
Publication Subtype Journal Article
Title Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array
Series title Canadian Journal of Fisheries and Aquatic Sciences
DOI 10.1139/cjfas-2017-0116
Volume 75
Issue 7
Year Published 2018
Language English
Publisher Canadian Science Publishing
Contributing office(s) Coop Res Unit Leetown
Description 9 p.
First page 1160
Last page 1168
Country Canada, United States
State British Columbia, Washington