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DNA Characterization of Three Collections of Snake River Fall Chinook (02GL, 02GK, & 02PH)

Category: Fish/Shellfish Research and Management - Fish/Shellfish Research

Date Published: December 2003

Number of Pages: 8

Author(s): Todd W. Kassler and James B. Shaklee


In 2002, scales from all unmarked/untagged (possibly “natural”) fish trapped and processed at Lyons Ferry Hatchery were collected to document the occurrence of hatchery and naturally reared fish in the collection. The unmarked/untagged fish trapped at Lyons Ferry Hatchery are thought to be predominantly from returns of unmarked/untagged fish (subyearlings) from the Nez Perce Tribe acclimation sites (Lyons Ferry Hatchery origin fish). If so, it would seem reasonable to use some of these fish in the Lyons Ferry Hatchery broodstock. Reading scales allows biologists to differentiate hatchery-produced from naturally produced (“wild”) fish but will not determine the specific origin of those hatchery fish because of similar sizes at release. This item is of great concern for fish management in the Snake River and Columbia River basins.

Beginning with subyearling releases by the Nez Perce Tribe in 1999, unmarked/untagged fall Chinook have been released above Lower Granite Dam. Some of these releases have associated CWT groups and some do not. Based on the tagging history of fish recovered from trapping efforts at Lyons Ferry Hatchery, biologists believe the majority of unmarked/untagged fish trapped at Lyons Ferry Hatchery are Snake River origin hatchery-produced fish that should not be genetically different than the Lyons Ferry Hatchery CWT groups.

In the future, it would be beneficial to compare the Umatilla stock and other Columbia River stocks to the Lyons Ferry Hatchery broodstock and the naturally produced Snake River stock to assess if the Lyons Ferry Hatchery program is maintaining the genetic integrity of the Snake River stock. In 2001 and 2002, the run of fall Chinook at Lower Granite Dam, in conjunction with large steelhead runs, effectively shut down the adult trap at times, which allowed stray fish to pass the dam. As a result, it is unknown at what level strays have been infused into natural production. These are all questions that may be answered in future studies.

The present study was undertaken to address two questions:

  1. Can scale samples from adults be successfully used for microsatellite DNA characterization of Snake River fall Chinook?
  2. How genetically similar are the following three groups of fish: a) unknown hatchery adults from subyearling releases (unmarked/untagged but verified as subyearling hatchery via scale analysis) volunteering into Lyons Ferry Hatchery, b) known Lyons Ferry Hatchery adults (broodstock), and c) known naturally produced adults of unknown origin sampled at Lower Granite Dam in 2002?

This memo summarizes the results of the microsatellite DNA analysis of three collections (02GL, 02GK, and 02PH) of fall-run Chinook salmon in the Snake River.