Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales.

ABSTRACT: The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

SUBMITTER: Chang SL 

PROVIDER: S-EPMC8699693 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature