Snake River Parentage Based Tagging

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 Methods.org: https://www.monitoringmethods.org/Method/Details/1432.

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 www.fishgen.net.

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.