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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #338806
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

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

Author
item LARSON, WESLEY - University Of Wisconsin
item Palti, Yniv
item Gao, Guangtu
item WARHEIT, KENNETH - Department Of Fish And Wildlife
item SEEB, JAMES - University Of Washington

Submitted to: Canadian Journal of Fisheries and Aquatic Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/17/2017
Publication Date: 7/1/2018
Citation: Larson, W.A., Palti, Y., Gao, G., Warheit, K.I., Seeb, J.E. 2018. 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. 75:1160-1168. doi:10.1139/cjfas-2017-0116.
DOI: https://doi.org/10.1139/cjfas-2017-0116

Interpretive Summary: Researchers from the USDA-ARS National Center for Cool and Cold Water Aquaculture have recently developed an assay called high-density single nucleotide polymorphism (SNP) array for genetic and genome-wide analyses in rainbow trout and steelhead, the ocean migrating form of rainbow trout. The new high density genetic assay has passed the quality control standards accepted for similar application by the Biotechnology industry and has been commercialized by Affymetrix. Previously we have demonstrated the utility of the assay to assess relationships between the DNA make-up of farmed rainbow trout and desired aquaculture production traits, which enabled accurate prediction of the genetic merit and breeding potential of the fish. Natural-origin steelhead in the Pacific Northwest USA are threatened by a number of factors including a potential erosion of genetic viability due to introgression from hatchery strains. In the current research, we collaborated with researchers from Washington State to evaluate the utility of the new assay for identifying a subset of SNPs that can differentiate hatchery and natural-origin populations in the Puget Sound to further study and reduce the potential negative impacts of the introgression between hatchery and natural origin fish. Our analyses identified 360 SNPs that are good candidate markers for differentiating between hatchery and natural steelehead fish in the Puget Sound, including a significantly higher number of SNPs than expected on two of the rainbow trout 29 chromosomes. Overall, the study demonstrated that the new high-density SNP array is a useful and valuable tool for population and conservation genomics studies in rainbow trout and steelhead.

Technical Abstract: Natural-origin steelhead 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. The major goal of this study was to use a recently developed SNP array containing ~57,000 SNPs to identify a subset of SNPs that can differentiate hatchery and natural-origin populations. We genotyped 35,765 polymorphic SNPs in nine populations of steelhead sampled from Puget Sound, Washington State, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (average FCT = 0.29, max = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (average FST = 0.25, max = 0.51). Comparisons with a linkage map for rainbow trout revealed that chromosomes Omy05 and Omy25 contained significantly more outliers than expected. These results indicate that the previously published conserved haplotype on Omy05 as well as structural differences in Omy25 may be of adaptive significance in the populations included in our study. We also explored the utility of the SNP array for genotyping duplicated loci and concluded that genotyping duplicated loci with this platform should be feasible. Our pilot study demonstrates that the 57K SNP array has a number of advantages compared to current genomics approaches and will be a valuable tool for population and conservation genomics studies in the future.