At-Sea Genetic Stock Identification in the Gulf of Alaska

Abstract Excerpt:
Pacific salmon (Oncorhynchus spp.) are usually found in mixed-stock schools in the ocean, meaning that fish from home streams as distant as North America and Asia might be found in the same school, making stock-specific management for conservation or harvest challenging (Wood et al. 1989). To overcome the challenges of mixed-stock management, stock identification methods such as genetic stock identification (GSI) using single nucleotide polymorphisms (SNPs) as markers are delivering high-throughput insights into the stock composition of salmon (Beacham et al. 2017, 2018; Miller et al. 1996). However, current GSI approaches based on second generation sequencing platforms (e.g., Illumina and Ion Torrent) mean that only sequencing large batches of individuals, known as “genotyping by the thousands” (GT-seq), is economically and practically feasible (Campbell et al. 2015; Beacham et al. 2017, 2018). These approaches require a specialized laboratory and several days turnover even under highly automated settings. For time and spatially sensitive stock identification, an in-field real-time SNP-based GSI approach with greater flexibility in sample batch size is desirable. Recent advances in third-generation single-molecule sequencing platforms like the Oxford Nanopore minION allow real-time sequencing on a pocket-sized portable sequencer (Mikheyev and Tin 2014; Quick et al. 2016). Here we develop and evaluate a novel Nanopore-based in-field SNP GSI method (termed nano-to-geno or “n2g”) by adapting existing technologies to the Nanopore platform. We used a concatenation approach to overcome low read numbers and high error rates inherent in the Nanopore platform (Cornelis et al. 2017; Schlecht et al. 2017).