Development of a powerful PlexSeq SNP panel for grandparentage studies for snake river fall chinook salmon

Authors: CAMPBELL, MATTHEW - Idaho Department Of Fish & Game; HARRIS, AUDREY - Pacific States Marine Fisheries Commission; ROBINSON, ZACHARY - Columbia River Intertribal Fish Commission; HORN, REBEKAH - Columbia River Intertribal Fish Commission; KAUFMAN, BENJAMIN - Agriplex Genomics; RICHARDS, KRISTEN - Agriplex Genomics; DELOMAS, THOMAS - US Department Of Agriculture (USDA)

Submitted to: Conservation Genetics Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/28/2026
Publication Date: 2/13/2026
Citation: Campbell, M.R., Harris, A., Robinson, Z.L., Horn, R.L., Kaufman, B., Richards, K., Delomas, T.A. 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.
DOI: https://doi.org/10.1007/s12686-026-01415-y

Interpretive Summary: There is concern that escaped aquaculture animals can interbreed with natural-origin animals and cause natural-origin populations to become genetically maladapted. A technique to identify natural-origin offspring of aquaculture animals by inferring grandparent-grandchild relationships was previously developed, but testing this technique requires a large SNP panel. This manuscript describes the development of a large SNP panel that can be used for validating the grandparent inference technique for monitoring reproduction of escaped aquaculture animals.

Technical Abstract: Interactions between hatchery-origin fish and wild populations raise concerns about genetic diversity, productivity, and ecological integrity. Monitoring effective hatchery straying, defined as the successful spawning of hatchery-origin fish in the wild, is essential, yet constrained by current genetic technologies. To address this, we developed a PlexSeq SNP genotyping panel for ESA-listed Snake River Fall Chinook Salmon to infer grandparent-grandchild relationships, enabling the detection of offspring produced by hatchery-origin strays. The panel comprises 1,684 loci split into two primer pools, integrating markers from existing GTseq panels alongside newly identified SNPs to enhance resolution. Following optimization, 1,157 loci were retained, yielding a mean heterozygosity of 0.286 and low false-positive error rates (<1e-18). This tool expands the capacity to assess hatchery impacts and informs management strategies aimed at conserving wild salmon populations.