Data from: Genotyping-in-Thousands by Sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

Here, we demonstrate a workflow for developing, evaluating, and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia, as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”.

Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2-backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~74% of which were B2-backcross or F2.

Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.

Methods

Genotyping-in-Thousands by sequencing (GT-seq) following Campbell et al. (2015) Molecular Ecology Resources as modified in Schmidt et al. (2020) Molecular Ecology Resources. Usage notes 342_RADseq_baseline.vcf: vcf file of genotypic data at 342 SNPs for all baseline individuals used for panel development 2016_and_2017_OKR_Onco.vcf: vcf file of genotypic data at 341 SNPs collected with GT-seq for 2016 and 2017 samples used for comparison with previous sequencing methods. 2019_OKR_Onco.vcf: vcf file of genotypic data at 341 SNPs collected with GT-seq for 2019 samples. 342_probeseqs_locusinfo.csv: text file containing sequences for the 342 loci where the retained SNPs are located, GT-seq genotyping input file Onco_biodata.xlsx: spreadsheet containing individual metadata for all samples used including sample identifiers, date of sample collection, body length, and sex