San Francisco Estuary and Watershed Science

California’s Feather River Hatchery (FRH) propagates two runs of Chinook salmon (Oncorhynchus tshawytscha): spring run and fall run. Loss of spawning habitat and historical hatchery practices have led to introgression of these runs. Recent efforts to reform hatchery operations at the FRH are focused on reducing introgression and increasing the proportion of natural-origin spawners in the broodstock. Implementing these reforms, however, requires a means of distinguishing FRH fish from natural-origin fish, and FRH spring-run fish from FRH fall-run fish. Coded-wire tagging and parentage-based genetic tagging can be used for this purpose, but are labor-intensive and expensive. Otolith thermal marking (OTM) is a 100% marking technique widely used in the Pacific Northwest, Alaska, and Russia that can be effective and relatively inexpensive. We initiated an OTM program at the FRH in 2005 to determine its viability as a 100% marking tool for a hatchery with an annual production goal of 10 million smolts. Our analysis of otoliths collected from returning adults at the FRH demonstrated that OTM could be successfully applied to identify the origin (FRH or natural) and, for FRH fish, the run type (spring run or fall run). Otoliths collected between 2009 and 2011 show run-type mixing between 12% to 20% in both spring-run and fall-run FRH broodstock. Additionally, results suggest natural-spawner contribution to hatchery broodstock is very low (<1% to 10%). OTM may provide another way to reduce the rate of introgression between FRH spring-run and fall-run Chinook salmon, and increasing the proportion of natural origin spawners in hatchery broodstock, both of which should improve the long-term viability of FRH spring-run and fall-run Chinook salmon.