Genotyping-in-Thousands by sequencing (GT-seq) genotyped data used for panel validation in GSI

Single Nucleotide Polymorphism (SNP) panels are powerful tools for
assessing genetic population structure and dispersal of fishes and can
enhance management practices for commercial, recreational, and subsistence
mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout
(Salvelinus fontinalis), and Lake Whitefish (Coregonus clupeaformis) are
amongst the most harvested and consumed fish species in northern
Indigenous communities in Canada, contributing significantly to food
security, culture, tradition, and economy. However, genetic resources
supporting Indigenous fisheries have not been widely accessible to
northern communities (e.g., Inuit, Cree, and Dene). Here, we developed
Genotyping-in-Thousands by sequencing (GT-seq) panels for population
assignment and mixed-stock analyses of three salmonids, to support
fisheries stewardship or co-management in northern Canada. Using
low-coverage Whole Genome Sequencing data from 943 individuals across
source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest
Territories), James Bay (Québec), and Mistassini Lake (Québec), we
developed a bioinformatic SNP filtering workflow to select informative SNP
markers from genotype likelihoods. These markers were then used to design
GT-seq panels, thus enabling high-throughput genotyping for these species.
The three GT-seq panels yielded an average of 413 autosomal loci and were
validated with an average assignment accuracy of 83.03%. Thus, these
GT-seq panels are powerful tools for assessing population structure and
quantifying the relative contributions of populations/stocks in mixed
stock fisheries across multiple regions. Interweaving these
genomic-derived tools with Traditional Ecological Knowledge will ensure
the sustainable harvest of three culturally important salmonids in
Indigenous communities, contributing to food security programs and the
economy in northern Canada.