A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon

Authors: ANDERSON, ERIC - Southwest Fisheries Science Center; CLEMENTO, ANTHONY - Southwest Fisheries Science Center; CAMPBELL, MATTHEW - Southwest Fisheries Science Center; PEARSE, DEVON - Southwest Fisheries Science Center; BEULKE, ANNE - Southwest Fisheries Science Center; COLUMBUS, CASSIE - Southwest Fisheries Science Center; CAMPBELL, ELLEN - Southwest Fisheries Science Center; Thompson, Neil; GARZA, JOHN - Southwest Fisheries Science Center

Submitted to: Evolutionary Applications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/17/2025
Publication Date: 5/13/2025
Citation: Anderson, E.C., Clemento, A.J., Campbell, M.A., Pearse, D., Beulke, A.K., Columbus, C., Campbell, E., Thompson, N., Garza, J.C. 2025. A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon. Evolutionary Applications. 18(5). Article e70110. https://doi.org/10.1111/eva.70110.
DOI: https://doi.org/10.1111/eva.70110

Interpretive Summary: Numerous ecological and biological questions that directly inform management of aquatic animal populations require the use of genetic tools. Such a case is found in Chinook salmon (Oncorhynchus tshawystcha) in California where multiple evolutionary lineages, ecotypes and populations exist at the southern extent of the species range. Management and conservation practices are predicated on genetic stock identification (i.e. population assignment) and in hatchery programs the use of parentage-based tagging for identifying parent-offspring relationships. In this study we developed a set of multi-allelic microhaplotype genetic markers for California Chinook salmon that can be applied comprehensively to assign lineage and migration timing ecotype to individual fish. The same microhaplotype panel has requisite variation to successfully assign parent-offspring and full-sibling relationship pairs, even in the winter-run population, which has reduced genetic diversity due to populations bottlenecks that occurred. The microhaplotype panel can be rapidly and inexpensively assayed and provides a single tool that has broad utility for investigation of Chinook salmon populations.

Technical Abstract: Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present, here, a novel set of multi-allelic microhaplotype genetic markers for Chinook salmon which provide unprecedented resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of microhaplotypes provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole genome sequence data, allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers have ample variation to accurately identify parent-offspring and full-sibling pairs in all California populations, including the genetically depauperate winter-run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods, also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.