Broodstock Sampling for PBT

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

Research
Project ID009 09 SC
Recovery DomainsInterior Columbia
Start Date01/04/2011
End Date05/15/2014
Year2009
StatusCompleted
Last Edited11/24/2021
 
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Description    


This project worked in combination/partnership with a Bonneville Power Administration funded project that is developing Parentage Based Tagging (PBT) technology in the Snake River Basin.

Through this project there were a total of seven semi-annual progress reports, one final report and two annual reports generated for a total of ten reports. More details are provided on the final report uploaded to the PCSRF Database. Because the work conducted at each worksite was the same and to avoid duplicating the reporting metrics on the database we have the split the reports by each worksite.

Through this project genetic samples of broodstock (steelhead and Chinook salmon) were collected at all Snake River (worksites) hatcheries during the 2011 – 2013 spawning seasons genotyped for the first PBT genetic baselines.

The following is a summary of the sampling by year and counts.
Steelhead hatchery broodstock Chinook salmon hatchery broodstock
2011 5,508 2011 8,710
2012 5,719 2012 8,768
2013 5,022 2013 9,153

Progeny from any of these parents (either collected as juveniles or adults), if genotyped, could be assigned back to their parents, thus identifying the hatchery they originated from and their exact brood year. By genotyping all parental broodstock, every juvenile is genetically tagged.

This project further addresses current and future objectives in creating PBT baselines within the Snake River Basin that can be used for monitoring harvest of hatchery stock and address additional effectiveness of hatchery integration programs.

The final outcome as a result of this project (past and future PBT projects) 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.

PBT technology will potentially remove coded-wire limitations such as: Physical tagging logistics, small sample size, high labor costs per unit, high cost, and potential physiological stress to the juveniles just prior to their release for downstream migrations.

Project Benefit    


This project will contribute samples to a BPA funded project aimed at developing new genetic technology that will mark hatchery stocks. This technology should benefit ESA listed Snake River steelhead and Chinook salmon. Successful implementation of a Parentage Based Tagging program could identify progeny of hatchery broodstock passing Lower Granite Dam, and thus significantly improve GSI estimates of stock composition of wild/hatchery adults in the Snake River drainage. It could provide an accurate estimate of mis-clip rates for all participating hatcheries. It could be used to conduct hatchery evaluations and reform, including acting as a tool to monitor variance in returns to each hatchery based on a wide range of hatchery practices.

Accomplishments

Metric Completed Originally
Proposed

Funding Details

SourceFunds
PCSRF$150,000
Other$62,148
Report Total:$212,148


Project Map



Worksites

Dworshak Clearwater FH    


  • Worksite Identifier: Dworshak Clearwater FH
  • Start Date: 01/04/2011
  • End Date: 05/15/2014
Area Description
Hatchery location

Location Information

  • Basin: Clearwater
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain: Interior Columbia
  • Latitude: 46.503757
  • Longitude: -116.320839

ESU

    No ESU data was found for this worksite.

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 42,429.00
    •      . . E.0.b
      Complement habitat restoration project
      0
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      NWPCC. 2005. Clearwater, Salmon, Snake/Hells Canyon subbasin plans. In, Columbia River Basin Fish and Wildlife Program. Portland, Oregon.
    •      . . E.0.d.1 Number of Cooperating Organizations 6
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      IDFG, WDFW, ODFW, NPT, SBT, USFWS
    •      . . E.0.e.1 Number of reports prepared 2
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, 3/30/11, PCSRF Report #1, IDFG, Boise, Idaho and Matt Campbell, 10/15/13, PCSRF Report #6, IDFG, Boiise, Idaho
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 42,429.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          The deliverables provided genetically sampled broodstock (steelhead and Chinook salmon) at Snake River hatcheries during the 2011 – 2013 spawning seasons. Genetic samples collected as part of this project were used as part of a Bonneville Power Administration (BPA) funded project aimed at developing Parentage Based Tagging (PBT) technology in the Snake River basin. During 2011 – 2013, approximately 5,500 hatchery steelhead and 9,000 hatchery Chinook salmon were sampled annually. See the attached final report for a table that provides the numbers of steelhead hatchery broodstock sampled for PBT. Development of parentage based tagging address objectives from the Snake/Hells Canyon, Clearwater, and Salmon subbasin plans: 1) Increase hatchery effectiveness for restoration and mitigation, 2) Gather and analyze harvest data to aid in run reconstruction to evaluate & status & action effectiveness, 3) Monitor effectiveness of hatchery & natural production measures; Basin-wide strategies: Strategy D.5 Harvest - Monitor inriver and ocean fisheries & routinely estimate stock composition & stock stock specific abundance, escapement, catch, and age distribution; Strategy D.6 Hydrosystem - Evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects o fish passage, and the connection between fish passage design and fish behavior. Monitor and evaluate effectiveness of actions taken to implement measures. Implement innovative hatchery actions to achieve restoration and mitigation objectives. Limiting Factors: The project addresses limiting factors associated with Population Traits - Impaired population conditions including genetic, life history, morphological, productivity, fitness, behavioral characteristics, and population size. Actions to address Population Traits identified in recommendations to amend the Columbia River Basin Fish and Wildlife Program include: 1) quantify salmon stray rates and potential genetic consequences, 2) develop genetic methods to assist management, 3) determine the reproductive contribution of hatchery fish, 4) determine the contribution of adult hatchery on spawning grounds.
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          Identification of hatchery steelhead & Chinook salmon parentage throughout Idaho

Rapid River Hatchery    


  • Worksite Identifier: Rapid River Hatchery
  • Start Date: 01/04/2011
  • End Date: 05/15/2014
Area Description
Hatchery location.

Location Information

  • Basin: Salmon
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain: Interior Columbia
  • Latitude: 45.354843
  • Longitude: -116.389572

ESU

    No ESU data was found for this worksite.

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 42,429.00
    •      . . E.0.b
      Complement habitat restoration project
      None
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      NPCC. Clearwater, Salmon, Snake/Hells Canyoun subbasin plans. 2005. In, Columbia River Basin Fish and Wildlife Program. Portland, OR.
    •      . . E.0.d.1 Number of Cooperating Organizations 6
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      IDFG, WDFW, ODFW, NPT, SBT, USFWS
    •      . . E.0.e.1 Number of reports prepared 1
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, 3/13/13, PCSRF Progress Report #5, IDFG, Boise, Idaho
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 42,429.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          The deliverables provided genetically sampled broodstock (steelhead and Chinook salmon) at Snake River hatcheries during the 2011 – 2013 spawning seasons. Genetic samples collected as part of this project were used as part of a Bonneville Power Administration (BPA) funded project aimed at developing Parentage Based Tagging (PBT) technology in the Snake River basin. During 2011 – 2013, approximately 5,500 hatchery steelhead and 9,000 hatchery Chinook salmon were sampled annually. See the attached final report for a table that provides the numbers of steelhead hatchery broodstock sampled for PBT. Development of parentage based tagging address objectives from the Snake/Hells Canyon, Clearwater, and Salmon subbasin plans: 1) Increase hatchery effectiveness for restoration and mitigation, 2) Gather and analyze harvest data to aid in run reconstruction to evaluate & status & action effectiveness, 3) Monitor effectiveness of hatchery & natural production measures; Basin-wide strategies: Strategy D.5 Harvest - Monitor inriver and ocean fisheries & routinely estimate stock composition & stock stock specific abundance, escapement, catch, and age distribution; Strategy D.6 Hydrosystem - Evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects o fish passage, and the connection between fish passage design and fish behavior. Monitor and evaluate effectiveness of actions taken to implement measures.Implement innovative hatchery actions to achieve restoration and mitigation objectives. Limiting Factors: The project addresses limiting factors associated with Population Traits - Impaired population conditions including genetic, life history, morphological, productivity, fitness, behavioral characteristics, and population size. Actions to address Population Traits identified in recommendations to amend the Columbia River Basin Fish and Wildlife Program include: 1) quantify salmon stray rates and potential genetic consequences, 2) develop genetic methods to assist management, 3) determine the reproductive contribution of hatchery fish, 4) determine the contribution of adult hatchery on spawning grounds.
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          Identification of hatchery steelhead and Chinook salmon parentage through-out the state of Idaho.

Oxbow Fish Hatchery    


  • Worksite Identifier: Oxbow Fish Hatchery
  • Start Date: 01/04/2011
  • End Date: 05/15/2014
Area Description
Samples collected at hatchery lat 46.624535 and Lon -17.07945, which shows the site as out of recovery domain. Updated the record to reflect the lab site to resolve the recovery domain issue.

Location Information

  • Basin: Lower Snake
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Washington
  • Recovery Domain:
  • Latitude: 46.624535
  • Longitude: -117.07945

ESU

    No ESU data was found for this worksite.

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 42,430.00
    •      . . E.0.b
      Complement habitat restoration project
      none
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      NPCC. 2005. Clearwater, Salmon, Snake/Hells Canyon subbasin plans. In, Columbia River Basin Fish and Wildlife Program. Portland, OR
    •      . . E.0.d.1 Number of Cooperating Organizations 6
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      IDFG, WDFW, ODFW, NPT, SBT, USFWS
    •      . . E.0.e.1 Number of reports prepared 1
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, 3/15/12, PCSRF Progress Report #3, IDFG, Boise, Idaho.
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 42,430.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          The deliverables provided genetically sampled broodstock (steelhead and Chinook salmon) at Snake River hatcheries during the 2011 – 2013 spawning seasons. Genetic samples collected as part of this project were used as part of a Bonneville Power Administration (BPA) funded project aimed at developing Parentage Based Tagging (PBT) technology in the Snake River basin. During 2011 – 2013, approximately 5,500 hatchery steelhead and 9,000 hatchery Chinook salmon were sampled annually. See the attached final report for a table that provides the numbers of steelhead hatchery broodstock sampled for PBT. Development of parentage based tagging address objectives from the Snake/Hells Canyon, Clearwater, and Salmon subbasin plans: 1) Increase hatchery effectiveness for restoration and mitigation, 2) Gather and analyze harvest data to aid in run reconstruction to evaluate & status & action effectiveness, 3) Monitor effectiveness of hatchery & natural production measures; Basin-wide strategies: Strategy D.5 Harvest - Monitor inriver and ocean fisheries & routinely estimate stock composition & stock stock specific abundance, escapement, catch, and age distribution; Strategy D.6 Hydrosystem - Evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects o fish passage, and the connection between fish passage design and fish behavior. Monitor and evaluate effectiveness of actions taken to implement measures. Implement innovative hatchery actions to achieve restoration and mitigation objectives. Limiting Factors: The project addresses limiting factors associated with Population Traits - Impaired population conditions including genetic, life history, morphological, productivity, fitness, behavioral characteristics, and population size. Actions to address Population Traits identified in recommendations to amend the Columbia River Basin Fish and Wildlife Program include: 1) quantify salmon stray rates and potential genetic consequences, 2) develop genetic methods to assist management, 3) determine the reproductive contribution of hatchery fish, 4) determine the contribution of adult hatchery on spawning grounds.
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          Identification of hatchery steelhead and Chinook salmon parentage throughout the state of Idaho.

Sawtooth Fish Hatchery    


  • Worksite Identifier: Sawtooth Fish Hatchery
  • Start Date: 01/04/2011
  • End Date: 05/15/2014
Area Description
Hatchery location

Location Information

  • Basin: Salmon
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain: Interior Columbia
  • Latitude: 44.151741
  • Longitude: -114.884293

ESU

    No ESU data was found for this worksite.

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 42,430.00
    •      . . E.0.b
      Complement habitat restoration project
      None
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      NWPCC. 2005. Clearwater, Salmon, Snake/Hells Canyon subbasin plans. In, Columbia River Basin Fish & Wildlife Program. Portland, OR.
    •      . . E.0.d.1 Number of Cooperating Organizations 6
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      IDFG, WDFW, ODFW, NPT, SBT, USFWS
    •      . . E.0.e.1 Number of reports prepared 3
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, 9/30/11, PCSRF Progress Report #2, IDFG, Boise, Idaho and Matt Campbell, 6/30/14, PCSRF Final Report, IDFG, Boise, Idaho and Steel, Anderson, Hess, N Campbell, Narum, and M Campbell, Annual Report 2011, IDFG, Boise, Idaho
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 42,430.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          The deliverables provided genetically sampled broodstock (steelhead and Chinook salmon) at Snake River hatcheries during the 2011 – 2013 spawning seasons. Genetic samples collected as part of this project were used as part of a Bonneville Power Administration (BPA) funded project aimed at developing Parentage Based Tagging (PBT) technology in the Snake River basin. During 2011 – 2013, approximately 5,500 hatchery steelhead and 9,000 hatchery Chinook salmon were sampled annually. See the attached final report for a table that provides the numbers of steelhead hatchery broodstock sampled for PBT. Development of parentage based tagging address objectives from the Snake/Hells Canyon, Clearwater, and Salmon subbasin plans: 1) Increase hatchery effectiveness for restoration and mitigation, 2) Gather and analyze harvest data to aid in run reconstruction to evaluate & status & action effectiveness, 3) Monitor effectiveness of hatchery & natural production measures; Basin-wide strategies: Strategy D.5 Harvest - Monitor inriver and ocean fisheries & routinely estimate stock composition & stock stock specific abundance, escapement, catch, and age distribution; Strategy D.6 Hydrosystem - Evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects o fish passage, and the connection between fish passage design and fish behavior. Monitor and evaluate effectiveness of actions taken to implement measures. Implement innovative hatchery actions to achieve restoration and mitigation objectives. Limiting Factors: The project addresses limiting factors associated with Population Traits - Impaired population conditions including genetic, life history, morphological, productivity, fitness, behavioral characteristics, and population size. Actions to address Population Traits identified in recommendations to amend the Columbia River Basin Fish and Wildlife Program include: 1) quantify salmon stray rates and potential genetic consequences, 2) develop genetic methods to assist management, 3) determine the reproductive contribution of hatchery fish, 4) determine the contribution of adult hatchery on spawning grounds.
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          Identification of hatchery steelhead & Chinook salmon parentage throughout Idaho

Pahsimeroi Fish Hatchery    


  • Worksite Identifier: Pahsimeroi Fish Hatchery
  • Start Date: 01/04/2011
  • End Date: 05/15/2014
Area Description
Hatchery location

Location Information

  • Basin: Salmon
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Idaho
  • Recovery Domain: Interior Columbia
  • Latitude: 44.689934
  • Longitude: -114.044716

ESU

    No ESU data was found for this worksite.

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 42,430.00
    •      . . E.0.b
      Complement habitat restoration project
      0
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
      NPCC. Clearwater, Salmon, Snake/Hells Canyoun subbasin plans. 2005. In, Columbia River Basin Fish and Wildlife Program. Portland, OR.
    •      . . E.0.d.1 Number of Cooperating Organizations 6
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      IDFG, ODFW, WDFW, NPT, SBT, USFWS
    •      . . E.0.e.1 Number of reports prepared 3
    •      . . E.0.e.2
      Name Of Report
      Matt Campbell, 10/30/12, PCSRF Progress Report #4, IDFG, Boise, Idaho and Matt Campbell, 4/15/14, PCSRF Progress Report #7, IDFG, Boise, Idaho and Steel, M Campbel, Ackerman, McCane, Hess, N Campbell and Narum, 2012, Annual Report, IDFG, Boise, Idaho
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 42,430.00
      •      . . . . E.2.b.2 tissue sampling and analysisY (Y/N)
        •      . . . . . . E.2.b.2.a
          Key issues addressed by tissue sampling and analysis research
          The deliverables provided genetically sampled broodstock (steelhead and Chinook salmon) at Snake River hatcheries during the 2011 – 2013 spawning seasons. Genetic samples collected as part of this project were used as part of a Bonneville Power Administration (BPA) funded project aimed at developing Parentage Based Tagging (PBT) technology in the Snake River basin. During 2011 – 2013, approximately 5,500 hatchery steelhead and 9,000 hatchery Chinook salmon were sampled annually. See the attached final report for a table that provides the numbers of steelhead hatchery broodstock sampled for PBT. Development of parentage based tagging address objectives from the Snake/Hells Canyon, Clearwater, and Salmon subbasin plans: 1) Increase hatchery effectiveness for restoration and mitigation, 2) Gather and analyze harvest data to aid in run reconstruction to evaluate & status & action effectiveness, 3) Monitor effectiveness of hatchery & natural production measures; Basin-wide strategies: Strategy D.5 Harvest - Monitor inriver and ocean fisheries & routinely estimate stock composition & stock stock specific abundance, escapement, catch, and age distribution; Strategy D.6 Hydrosystem - Evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects o fish passage, and the connection between fish passage design and fish behavior. Monitor and evaluate effectiveness of actions taken to implement measures.Implement innovative hatchery actions to achieve restoration and mitigation objectives. Limiting Factors: The project addresses limiting factors associated with Population Traits - Impaired population conditions including genetic, life history, morphological, productivity, fitness, behavioral characteristics, and population size. Actions to address Population Traits identified in recommendations to amend the Columbia River Basin Fish and Wildlife Program include: 1) quantify salmon stray rates and potential genetic consequences, 2) develop genetic methods to assist management, 3) determine the reproductive contribution of hatchery fish, 4) determine the contribution of adult hatchery on spawning grounds.
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          Identification of hatchery steelhead & Chinook salmon parentage throughout Idaho