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.