Genetic Stock Identification of Snake River Steelhead at Lower Granite Dam, 2008-2011

Genetic stock identification (GSI) using single nucleotide polymorphisms (SNPs) has been conducted successfully in the lower Columbia River and elsewhere throughout the Pacific Rim to estimate stock contributions in salmon and steelhead mixtures. Here, we present a SNP baseline for natural origin steelhead in the Snake River and use variation at SNPs to estimate the stock composition of adults passing Lower Granite Dam. Our goals in this study were two-fold: 1) document the genetic structure of steelhead in the Snake River Basin using SNPs, and 2) estimate the composition (and abundance) of natural origin stocks migrating past Lower Granite Dam. To estimate stock compositions, tissues were collected from adults captured at the Lower Granite Dam adult trap throughout the run and genotyped at 192 SNPs including a Y-specific allelic discrimination assay that differentiates sex in O. mykiss. Results indicate that GSI using SNPs should greatly assist managers in assessing the viability of natural origin steelhead in the Snake River Basin. GSI can be used to inform run-reconstruction models and provide essential information for estimating Viable Salmonid Population parameters including abundance, population productivity, sex ratios, and diversity.