Snake River Parentage Based Tagging

Salmonid Research, Monitoring, and Evaluation (RM&E)

Project ID015 12 SR
Recovery Domains -
Start Date01/01/2014
End Date03/31/2017
Last Edited05/08/2024
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Fisheries technicians genetically sample steelhead and Chinook salmon broodstock at Snake River hatcheries. Technicians also assisted IDFG/EFGL personnel in organizing, inventorying, and processing samples at the Eagle Fish Genetics lab.

This work contributed to an on-going BPA funded project (#2010-031-00) that is implementing a new, powerful genetic technology that should be cheaper and more efficient than coded-wire tags for monitoring steelhead and Chinook salmon in the Snake River basin. This technology, called Parentage Based Tagging, should provide a better tool to meet PCSRF objectives associated with marking hatchery stocks, conducting hatchery evaluations and reform, and enforcing salmonid fishery management measures. It should also provide a more powerful tool to address needs in multiple “Reasonable and Prudent Alternatives” (RPA) in the BiOp.

In the fall of 2013, the Northwest Power Planning Council recommended to the Bonneville Power Administration that PBT in the Snake River basin receive continued funding for the next 5-10 years to assess its effectiveness and efficiency for broader application throughout the Columbia River basin.

Over the projects performance period, fisheries technicians assisted with the sampling, organization, and inventory of >20,000 hatchery steelhead and >28,000 hatchery Chinook salmon in the Snake River basin.

The actual project metrics implemented fall under the work type titled “tissue sampling and analysis” and involved the tissue sampling of hatchery steelhead and spring/summer Chinook broodstock spawned in the Snake River basin. Fisheries technicians ensured that genetic samples came from fresh, “live” tissue and that samples were properly preserved until DNA extraction. They also ensured that samples were properly labeled and inventoried and that data/information from every fish sampled was recorded and linked to a field/hatchery sample number (sample/spawn date, take #, hatchery, sex, length, cross information, etc.) and a unique genetic number. Methods for sampling hatchery broodstock are published on Monitoring

The genetic samples collected as part of this PCSRF project are used in an on-going BPA funded project (#2010-031-00) implementing parentage based tagging in the Snake River basin. Tissue samples are genotyped with sets of 96 single nucleotide polymorphism (SNP) genetic markers to build parental genetic baselines which provides genetic tagging of millions of hatchery-origin fish from the Snake River basin. These baselines are available on

Project Benefit    

One of the major goals of the PCSRF program is to improve management practices to maintain healthy salmon populations and prevent decline of ESA-listed salmon. This project will contribute samples to a BPA funded project implementing new genetic technology that permanently genetically marks hatchery stocks. This technology should benefit monitoring of ESA listed Snake River steelhead and Chinook salmon. Continued implementation of this technology in the Snake River basin will allow managers to estimate the number of Snake River steelhead and Chinook salmon contributing to out-of-state and in-state fisheries; estimate run-timing and harvest of individual hatchery stocks; and assess straying of hatchery adults into wild/natural populations. It will also allow more accurate estimates of wild escapement to the Snake River basin, since unmarked hatchery adults can be reliably detected and their proportions estimated.


Metric Completed Originally

Funding Details

Report Total:$211,235

Project Map


Snake River Basin    

  • Worksite Identifier: Snake River Basin
  • Start Date: 01/01/2014
  • End Date: 03/31/2017
Area Description
Snake River Basin

Location Information

  • Basin: Middle Snake-Boise (170501)
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain:
  • Latitude: 43.67744
  • Longitude: -116.40274


  • Snake River Basin Steelhead DPS
  • Snake River Fall Chinook Salmon ESU
  • Snake River Spring/Summer-run Chinook Salmon ESU




  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 211,235.00
    •      . . E.0.b
      Complement habitat restoration project
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      2008 FCRPS Biological Opinion Includes the following components: Parentage Based Tagging technology addresses recommended Research, Monitoring and Evaluation (RM&E) Strategies called for under NOAA’s Fisheries Federal Columbia River Power System Biological Opinion (BiOp) ( This includes: • RPA 55.8-Evaluate new tagging technologies for use in improving the accuracy and assessing delayed or indirect hydro effects on juvenile or adult fish. • RPA 50.5- Provide additional status monitoring to ensure a majority of Snake River B-Run steelhead populations are being monitored for population productivity and abundance: “Obtain DNA fingerprint of each hatchery stock so that they can be detected passing through the fisheries and into the spawning grounds”… • RPA 50.7-Fund marking of hatchery releases from Action Agencies’ funded facilities to enable monitoring of hatchery origin fish in natural spawning areas and the assessment of status of wild populations. • RPA 62.5-Investigate the feasibility of genetic stock identification monitoring techniques. The development of new PBT genetic tagging technology has also been directly called for by both the Pacific Salmon Commission and the Independent Scientific Review Panel and Advisory Boards (;
    •      . . E.0.d.1 Number of Cooperating Organizations 7
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
    •      . . E.0.e.1 Number of reports prepared 9
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, Idaho OSC PCSRF NOAA Progress Reports (6), Idaho OSC PCSRF NOAA Final Report (1) Idaho Craig Steele, Jesse McCane, Michael Ackerman , Ninh Vu and Matt Campbell, January 2016, Parentage Based Tagging of Snake River Hatchery Steelhead and Chinook Salmon, Annual Progress Report, IDFG Report # 16-02, IDFG, Boise, Idaho Matthew Campbell, Craig Steele, and Lance Hebdon, March 15, 2016, ESA Biological Opinion Reasonable and Prudent Alternative BPA 2010-031-00, IDFG Boise, Idaho
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 211,235.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          Broodstock at all Snake River hatcheries are sampled annually for genetic monitoring
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          PBT is used for a variety of monitoring purposes including identifying the origin and age of fish harvested in mixed-stock fisheries or that stray into natural spawning areas, as well as generating detailed stock-specific information on broodstock demographics and heritability of specific traits.