A Microsatellite DNA Analysis of Snake River fall-run Chinook (2002 & 2003)

Genetic characteristics of Chinook salmon within the Snake River and Columbia River basins have been examined extensively (Blankenship et al. 1997, Blankenship and Mendel 1994, Bugert et al. 1995, LaVoy and Mendel 1996, Marshall et al. 1995, Marshall et al. 2000, Utter et al. 1982, and Utter et al. 1995). A spring/summer-run of Chinook salmon and a fall-run were determined to be in separate ESUs (Waples 1991) and Snake River fall-run Chinook salmon were listed as threatened under ESA in 1992 (NMFS 1992). Management and conservation of these stocks have, therefore, been of interest to biologists in the Snake River Basin.

Returns of Chinook salmon trapped at Lyons Ferry Hatchery (LFH) include adipose clipped CWT fish that are determined to be hatchery broodstock, unmarked/untagged fish that volunteer to the hatchery, and marked/tagged strays from other hatcheries. The unmarked/untagged fish could be of hatchery origin or naturally reared origin. 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 and scale patterns. Straying of hatchery origin salmon into the Snake River has been documented at Lyons Ferry Hatchery (Milks et al. 2003, Bugert et al. 1991). Scale patterns also allow for the identification of Chinook released from the hatchery as subyearlings and yearlings (Connor et al. In Press).

The unmarked/untagged hatchery origin subyearling Chinook that return to Lyons Ferry Hatchery are thought to be predominantly from the Nez Perce Tribe (NPT) acclimation sites (Lyons Ferry Hatchery origin fish; Debbie Milks, WDFW personal communication). The unmarked/untagged hatchery origin yearling Chinook that return to Lyons Ferry Hatchery (included in the samples from 2002 and 2003) are thought to be out-of-basin strays because all of the yearling releases from Lyons Ferry Hatchery are adipose clipped, coded wire tagged, and VIE (visual implanted elastomer) tagged.

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 hatchery origin stray fish to pass the dam. As a result, it is unknown at what level strays have been infused into natural production in the Snake River Basin. Historically, the Umatilla Hatchery program was the major contributor of stray fall-run Chinook to the Snake River. Genetic comparison of the Umatilla Hatchery broodstock to the Lyons Ferry Hatchery broodstock would help determine how effectively the Lyons Ferry Hatchery program is maintaining the genetic integrity of the Snake River stock. Additional analysis of the naturally produced Chinook collected at Lower Granite Dam and of the Umatilla Hatchery broodstock would indicate if strays from the Umatilla Hatchery are impacting the naturally spawning Snake River stock.

A growing number of studies have used variation at microsatellite DNA loci to investigate stock structure (Small et al. 1998, Beacham et al. 1999, Shaklee et al. 1999, Balloux and Lugon-Moulin 2002, Beacham et al. 2003, and Beacham et al. 2004). Microsatellite markers typically exhibit high numbers of alleles and high heterozygosities, and are, therefore, statistically powerful markers to characterize stocks, estimate interrelationships among populations, and analyze mixtures. Microsatellite loci are tandemly repeated arrays of short (commonly di-, tri-, and tetra-nucleotide) sequences and are considered to be non-coding in that they do not encode RNA or proteins, and, therefore, are assumed to be selectively neutral.

Because these DNA markers offer the potential of higher resolution analyses, WDFW initiated a study of microsatellite DNA variation in the Snake River fall-run Chinook to characterize groups of fish relevant to the Lyons Ferry Hatchery: Lyons Ferry Hatchery broodstock, unmarked/untagged adults from yearling and subyearling releases that volunteered to Lyons Ferry Hatchery, unmarked/untagged adults of natural origin from collections at Lower Granite Dam in 2002 and 2003, and Umatilla Hatchery broodstock to conduct the following analyses:

1. Pairwise analyses from collections made in 2002: adults from Lyons Ferry Hatchery (LFH) broodstock, unmarked/untagged hatchery adults volunteering to Lyons Ferry Hatchery (yearling and sub-yearling releases), and adults of natural origin sampled at Lower Granite Dam (LGD).
2. Pairwise analyses from collections made in 2003: adults from Lyons Ferry Hatchery (LFH) broodstock, unmarked/untagged hatchery adults volunteering to Lyons Ferry Hatchery (yearling and sub-yearling releases), and adults of natural origin sampled at Lower Granite Dam (LGD).
3. Pairwise analyses of Umatilla Hatchery broodstock 2003 to the collections made in 2002 and 2003.

Microsatellite DNA loci are valuable genetic markers not only because of their high levels of genetic variability but also because they (like other DNA markers) can be analyzed using fin clip and other non-lethal biopsy samples. Non-lethal methods may prove to be essential for this application because of the critically low abundance of the Snake River fall-run Chinook stock.