Grandparent Inference from Genetic Data

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

Project ID011 21 SC
Recovery Domains -
Start Date12/09/2021
End Date11/15/2024
Last Edited04/26/2022
1 - 1


The Grandparent Inference from Genetic Data project will develop and test a new genetic technology for monitoring potential genetic risks posed from straying hatchery fish. This new technology extends the methodology of Parentage Based Tagging (PBT) to identifying the grandchildren of hatchery fish produced in the wild. In doing so, it could provide a complementary tool for current monitoring requirements that involve estimating the proportion of hatchery-origin fish on natural-spawning grounds (pHOS). To assess the feasibility of grandparentage testing, IDFG will study that will be completed in 3 phases:

• Phase one: Genetic Marker Panel Development- Develop a new genetic marker panel with adequate power for grandparentage analyses.

• Phase two: Genetic Analysis- Genotype hatchery broodstock samples to build grandparentage baseline (~12,500 samples) and ~500 known hatchery grandchildren for error testing.

• Phase three: Wild Salmonid Tagging/Marking Study- Genotype wild adults sampled at Lower Granite Dam (~1,800 samples) to provide empirical estimates of assignment rates, error, and the proportion of natural origin steelhead returning to the Snake River basin that “wild” fish that were produced by Wild x Wild, Wild x Hatchery, and Hatchery x Hatchery crosses.

Project Benefit    

Quantifying straying in salmonid populations is difficult, particularly for steelhead that return to spawn on the peak of spring snowmelt when water flows are high and water is turbid. In addition, their iteroparous life-history means that few carcasses are available

for recovery. These factors preclude the use of typical monitoring methods such as weir trapping and spawning ground surveys (Campbell et al 2012). Even if identifying and enumerating straying hatchery steelhead was possible, the major genetic concerns involve

whether those fish successfully spawn with wild fish. If the feasibility of Grandparentage testing technology is demonstrated, this will provide a powerful new tool for monitoring risks posed from straying hatchery fish. This type of monitoring is directly called for in

the NMFS recovery plan for Snake River steelhead (NMFS 2017).


Metric Completed Originally

Funding Details

Report Total:$142,210

Project Map


Eagle Fish Genetics Lab    

  • Worksite Identifier: Eagle Fish Genetics Lab
  • Start Date: 12/09/2021
  • End Date: 11/15/2024
Area Description

No Area Description data was found for this worksite.

Location Information

  • Basin: Middle Snake-Boise
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain:
  • Latitude: 43.67729
  • Longitude: -116.40316


  • Snake River Basin Steelhead DPS




  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding .00
    •      . . E.0.b
      Complement habitat restoration project
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
    •      . . E.0.d.1 Number of Cooperating Organizations
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
      •      . . . . E.2.b.6 Wild salmonid tagging/marking studyY (Y/N)
        •      . . . . . . E.2.b.6.a
          Key issues addressed by wild salmon tagging/marking study
        •      . . . . . . E.2.b.6.b Number by species of wild salmonids tagged/marked (LOV)