Dense SNP panels resolve closely related Chinook salmon populations

Abstract

Chinook salmon (Oncorhynchus tshawytscha) are migratory fish that are highly valued for subsistence, sport, and commercial fisheries throughout their native range. Populations of Chinook salmon in western Alaska have exhibited long-term declines, leading to restrictions on harvests. Management priorities require greater resolution for genetic stock identification (GSI) than is available with current methods. We leveraged RADseq, TaqMan, and GT-seq data originating from multiple sources, collected through time, to develop a set of GT-seq panels containing 1092 single nucleotide polymorphisms (SNPs) that improved GSI resolution in western Alaska for at-sea and in-river sampling. We generated a dense linkage map to ensure that markers selected for panels spanned the entire genome. In addition, we identified multiple RADseq markers that were associated with sex; these aligned to a 5-centimorgan (cM) region on the sex chromosome. Finally, we developed a bioinformatic pipeline to streamline analysis of GT-seq data that is capable of genotyping microhaplotypes and paralogs, both of which can improve GSI resolution over traditional single-SNP data. Our panels and pipeline provide tools for management agencies to rapidly and easily analyze large-scale genotyping projects.

A GT-seq panel for walleye (Sander vitreus) provides a generalized workflow for efficient development and implementation of amplicon panels in non-model organisms

“…Finally, researchers conducting GT-seq must consider trade-offs associated with different genotyping approaches. The two main approaches we are aware of are: (1) in-silico probe-based methods that use pattern matching to genotype specific alleles (Campbell et al, 2015; McKinney et al, 2019) and (2) alignment-based methods that call all polymorphisms in a given amplicon (Baetscher et al, 2019). A major advantage of probe-based methods is that databases of probes can be shared among laboratories, facilitating standardization.…”

“…GT-seq and other amplicon sequencing methods have tremendous potential for facilitating high-throughput genotyping in non-model organisms (Meek & Larson, 2019). Few published studies, however, have critically analyzed the panel development process (see McKinney et al 2019). Here, we leverage our experiences developing a GT-seq panel for walleye with testing various aspects of the GT-seq methodological process to provide general guidelines usable by other researchers to simplify panel construction and validation, particularly in non-model species.…”

“…Smaller ascertainment datasets are likely sufficient when the main applications of a given GT-seq panel are kinship analysis and GSI of highly diverged populations; however, when designing GT-seq panels to differentiate closely related populations (e.g. Chinook salmon Oncorhynchus tshawytscha in western Alaska), accurate characterization of ascertainment populations is vital (Larson et al, 2014; McKinney et al, 2019).…”

“…Moreover, developing GT-seq panels is a relatively involved task and, to this point, there are limited resources providing standardized workflows and guidelines for efficient panel construction (but see Campbell et al, 2015; McKinney et al, 2019). At a basic level, panel construction involves SNP discovery, SNPs selection, primer design, and panel optimization (see Baetscher et al, 2018; McKinney et al, 2019; Schmidt et al, 2019); however, within this general framework there are many decision points in panel development related to primer selection, multiplexing approaches, laboratory protocols, and analysis parameters that have yet to be addressed. We used walleye ( Sander vitreus ) from Minnesota and Wisconsin, USA, as a test case to investigate various tradeoffs associated with GT-seq panel development and optimization and leveraged our collective experience to provide guidelines for researchers developing GT-seq panels.…”

“…While GT-seq panels have been developed to maximize accuracy for GSI (McKinney et al, 2019) or parentage (Baetscher et al, 2018) analyses, the potential for developing dual-purpose panels is largely unexplored. Moreover, developing GT-seq panels is a relatively involved task and, to this point, there are limited resources providing standardized workflows and guidelines for efficient panel construction (but see Campbell et al, 2015; McKinney et al, 2019).…”