Genotyping by Sequencing

This project funded research of Genotyping by Sequencing (GBS) platforms and protocols, the purchase of a NextSeq sequencer and associated laboratory equipment necessary for GBS, and genotyping of samples using the NextSeq sequencer. The purchased equipment was used for real-time Sockeye (Oncorhynchus nerka) broodstock genotyping, the genotyping of wild steelhead (O. mykiss) and Chinook salmon (O. tshawytscha) at Lower Granite Dam for Genetic Stock Identification and the estimation of stock specific abundance, the genotyping of hatchery steelhead and Chinook salmon in the Snake River basin to provide 100% Parent Based Tagging (PBT).

The genetic baselines for steelhead and salmon developed as part of this work allows the genetic monitoring of wild and hatchery salmonid populations throughout the Salmon River drainage in Idaho. The mainstem Salmon River is approximately 425 miles in length. Genetic baselines are used for genetic stock identification to estimate wild population viability metrics (abundance, productivity, spatial structure, and diversity). These viable salmonid population (VSP) metrics are used by NOAA for determining the conservation status of populations and larger-scale groupings of Pacific salmonids. As a specific application, the VSP approach is intended help in the establishment of Endangered Species Act (ESA) delisting goals.

The work funded as part of this project contributes to three ongoing Bonneville Power Administration projects (2007-402-00 Sockeye Genetic Stock Identification, 2010-26-00 Salmon and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam, and 2010-031-00 Snake River Chinook and Salmon Parental Based Tagging).

This project will provide new, cost and time efficient equipment for three exisiting BPA funded projects that benefit ESA-listed salmon and steelhead populations in the Snake River basin. These three projects include:
-2007-402-00 Redfish Lake Sockeye Salmon Captive Broodstock Program
-2010-026-00 Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
-2010-031-00 Snake River Chinook and Steelhead Parental Based Tagging

These projects directly address PCSRF program priorities associated with:
-Maintaining populations while limiting factors are being addressed
-Status monitoring programs that directly contribute to population viability
-Monitoring necessary for the exercise of tribal treaty fishing rights or native subsistence fishing on salmon and steelhead