Data Repository for Salmon and Steelhead Genetic and Metadata

Salmonid Restoration Planning and Assessments

Project ID	007 11 SC
Recovery Domains	-
Start Date	01/01/2013
End Date	07/31/2015
Year	2011
Status	Completed
Last Edited	05/01/2025

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Description

The development of an Operational Web-based, GIS-interfaced, relational database (www.fishgen.net) capable of uploading and exporting genetic data and metadata according to standardized templates and formats has been completed. The GIS Map interface allows for searching, displaying and selecting sample collections in the database and associated metadata. Genetic Stock Identification and Parentage Based Tagging baselines for Snake River steelhead and Chinook salmon are now securely stored and publicly available on this repository.

The results of this project address the design and maintenance of databases used for adult salmonid population monitoring, harvest monitoring, and research projects aimed at addressing salmonid life history or management questions focused on salmonid restoration and sustainability.

This project will support long-term status and trend monitoring of Snake River spring/summer Chinook salmon and steelhead by providing fa permanent and publically available repository for genetic and metadata for these species. Long-term status and trend monitoring is a component of the RME (chapter 9) portion of the Proposed ESA Recovery Plan for Snake River Idaho Spring/Summer Chinook Salmon and Steelhead. (Nov 2015).

Project Benefit

This project supports PCSRF goals for marking hatchery stocks (and developing new marking technology); conducting hatchery evaluations and reform; and conducting fishery evaluations and assessments. This project will benefit all State, Federal and Tribal agency recovery efforts for Pacific salmon and steelhead listed under the Endangered Species Act that use or anticipate using standardized genetic baselines for Genetic Stock Identification and Parentage Based Tagging. Both of these new genetic technologies are endorsed by the Councils Fish and Wildlife Program, the ISRP and ISAB, and the Pacific Salmon Commission. These projects can provide information on wild population viability metrics (abundance, productivity, spatial structure, and diversity), inform survival, straying, and harvest rates on hatchery fish by stock, rearing facility, and release location, and evaluate the effects that hatchery reform actions have on the recovery of salmon and steelhead populations.

Source

Funds

PCSRF

$296,014

Other

$100,000

Report Total:

$396,014

Worksites

IDFG, Eagle Fish Genetics

Worksite Identifier: IDFG, Eagle Fish Genetics
Start Date: 01/01/2013
End Date: 07/31/2015

Area Description
Snake River Basin

Location Information

Basin: Middle Snake-Boise (170501)
Subbasin: Lower Boise (17050114)
Watershed:
Subwatershed:

State: Idaho
Recovery Domain:
Latitude: 43.67787
Longitude: -116.40303

ESU

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

Map

Photos

Metrics

B.0 Salmonid Restoration Planning and AssessmentsY (Y/N)

. . B.0.a Planning And Assessment Funding 396,014.00
. . B.0.b.1 Area Encompassed .1

. . B.1 Restoration Planning And CoordinationY (Y/N)

. . . . B.1.a Planning and Coordination funding 396,014.00

. . . . B.1.b.10 Designing or maintaining restoration data systemsY (Y/N)

. . . . . . B.1.b.10.a

Name of plan implemented
NMFS. Nov 2015. Draft ESA Recovery Plan for Idaho Snake River Spring/Summer Chinook Salmon (Oncorhynchus tshawytscha) and Snake River Steelhead (Oncorhynchus mykiss) Populations. NMFS West Coast Region Portland, Oregon

. . . . . . B.1.b.10.b

Description and scope of the plan implemented

This project will support long-term status and trend monitoring of Snake River spring/summer Chinook salmon and steelhead by providing a permanent and publicly available repository for genetic and metadata for these species. Long-term status and trend monitoring is a component of the RME (chapter 9) portion of the Proposed ESA Recovery Plan for Snake River Idaho Spring/Summer Chinook Salmon and Steelhead. (Nov 2015) The genetic database will serve as a final genetic repository for fisheries genetic data (hatchery and wild) produced and published by the Department, hold records from potentially hundreds of thousands of samples. It will be built in a way that it could be scalable to incorporate additional labs and genetic data for the entire Columbia River basin (and ultimately a range-wide database). It will be accessible over the internet, such that multiple organizations could have restricted or full access. The database will have a very user-friendly interface and protocol for submitting standardized genetic data (any locus, any number of alleles) and standardized metadata. The interface must allow user data to be submitted without requiring manual inspection from a curator. The database will have a built in web-based GIS-interface, for searching, displaying and selecting sample collections in the database and associated metadata, and to produce simple maps. The database will have a very user-friendly interface and protocol for exporting genetic and metadata from the database. The database will have a built in interface with 3rd party genetic software programs (e.g. GSI_SIM; http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=12964, and SNPPIT; http://swfsc.noaa.gov/textblock.aspx?Division=FED&ParentMenuId=54&id=16021) that are used for genetic parentage and genetic stock assignment or allow very easy export of data in the format needed for these programs. The database will house data that would be available to the public within a reasonable time-frame agreed to by user labs. This will likely be accomplished through a “release date” field within the submission table that would allow the user to select either “release immediately” or to hold for some specified period of time. The idea being that the latter option would allow the user time to write their own report or manuscript describing the data prior to the data being released.