Development of a Powerful PlexSeq™ SNP Panel for Grandparentage Studies for Snake River Fall Chinook Salmon
Abstract
Interactions between hatchery-origin fish and wild populations of salmonids raise concerns about genetic diversity, productivity, and ecological integrity. Monitoring hatchery-origin reproduction in natural populations is essential but constrained by existing genetic technologies, particularly when hatchery adults stray and reproduce outside of sampled spawning facilities. To address this limitation, we developed a high-density PlexSeq™ SNP panel for ESA-listed Snake River Fall Chinook Salmon to support grandparent-grandchild inference. The panel integrates loci from existing GTseq panels with newly identified SNPs to increase marker density while maintaining compatibility with established baselines. Following multiplex optimization and filtering, 1,157 polymorphic loci were retained. Sequencing depth and allele balance metrics demonstrated consistent amplification and reliable genotype classification. Monte Carlo simulations indicated low false-positive error rates and false-negative rates below 0.01. This panel expands capacity to detect hatchery-origin reproduction across generations and provides a practical tool for fisheries managers seeking to quantify hatchery influence on natural populations.
Authors
Citation
Campbell, M. R., A. C. Harris, Z. L. Robinson, R. L. Horn, S. R. Narum, B. Kaufman, K. Richards, and T. A. Delomas. 2026. Development of a powerful PlexSeq™ SNP panel for grandparentage studies for snake river fall Chinook salmon. Conservation Genetics Resources 18:8. https://doi.org/10.1007/s12686-026-01415-y