Rapid Genetic Identification of Chinook Salmon Runs for the Central Valley Spring Run Juvenile Production Estimate (SRJPE)

SR-JPE EDI Data Package Abstract The California Central Valley supports four seasonal runs of Chinook salmon ( Oncorhynchus tshawytscha ): fall, late fall, spring, and winter. Spring-run Chinook have declined substantially due to habitat loss and anthropogenic climate change and are listed as threatened under both the California Endangered Species Act and the federal Endangered Species Act. In 2021, the California Department of Water Resources (DWR) and its partners launched the Spring-Run Juvenile Production Estimate (SRJPE) to meet regulatory requirements for long-term operations of the California State Water Project. The SRJPE estimates the annual abundance of natural-origin spring-run juveniles entering the Sacramento-San Joaquin Delta during outmigration. Accurate run identification is critical to this effort and is achieved using two genetic approaches: CRISPR-based SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) and genotyping-in-thousands by sequencing (GT-seq). This EDI data package provides genetic run assignments for outmigrating juvenile Chinook salmon collected at 11 sites across the Sacramento River Basin from water years 2022–2026. Associated data include capture date, fork length, and length-at-date (LAD)–based run assignments.