Oncorhynchus kisutch genetic stock ID SNP baseline

Genetic stock identification (GSI) using genotypes produced from
genotyping-by-sequencing of SNP loci has become the gold standard for
stock identification in Pacific salmon, which are found in mixed stocks in
the ocean. Sequencing platforms currently applied require large batch
sizes and multi-day processing in specialized facilities to perform
genotyping by the thousands. However, recent advances in third-generation
single-molecule sequencing platforms, like the Oxford Nanopore minION,
provide base calling on portable, pocket-sized sequencers and promise
real-time, in-field stock identification on variable batch sizes. Here we
evaluate utility and comparability to established GSI platforms of at-sea
stock identification of coho salmon Oncorhynchus kisutch based on targeted
SNP amplicon sequencing on the minION platform during a high-sea winter
expedition to the Gulf of Alaska. As long read sequencers are not
optimized for short amplicons, we concatenate amplicons to increase
coverage and throughput. Nanopore sequencing at-sea yielded stock
assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls
agreed with Ion Torrent based genotypes in 83.25%, but assignment of
individuals to stock of origin only agreed in 61.5% of individuals
highlighting inherent challenges of Nanopore sequencing, such as
resolution of homopolymer tracts and indels. However, poor representation
of assayed coho salmon in the queried baseline dataset contributed to poor
assignment confidence on both platforms. Future improvements will focus on
lowering turnaround time, accuracy, throughput, and cost, as well as
augmentation of the existing baselines. If successfully implemented,
Nanopore sequencing will provide an alternative method to the large-scale
laboratory approach by providing mobile small batch genotyping to diverse
stakeholders.