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SNP amplicons results of 50 hybrid Chinook-Coho salmon

Citation

Araujo, Andres (2022), SNP amplicons results of 50 hybrid Chinook-Coho salmon, Dryad, Dataset, https://doi.org/10.5061/dryad.b8gtht7c4

Abstract

These SNP panel results confirm the hybrid origin in 50 Chinook-Coho Salmon individuals. The SNP panel is composed of two amplicons and five diagnostic SNPs. DNA amplicons OkiOts_120255 and Oki_RAD41030 have SNP sites fixed for alternate base pairs in Chinook and Coho salmon (Beacham and Wallace 2019). The panel examined genotypes at one diagnostic position in OkiOts_120255 SNP: 113 (Reference=A, Variant=C) and four positions in Oki_RAD41030: 45 (TC), 51(CG), 195 (GA), and 198 (TG) called via Proton software Variant Caller®. The hybrid salmon were heterozygous for a Chinook and Coho haplotype at both SNP loci, confirming these as the parental species involved in the hybridization and consistent with all being F1 or higher order (F2 or back-cross) hybrid individuals. 

Beacham, T. D. & Wallace, C. G. (2019). Salmon species identification via direct DNA sequencing of single amplicons. Conservation Genetics Resources, 1-7. https://doi.org/10.1007/s12686-o19-01102-1.

Methods

DNA from the suspected hybrids was loaded on a P1 chip v3 and run consecutively on the Ion Chef, and subsequently loaded on an Ion Torrent Proton sequencer (both machines by Thermo Fisher Scientific Inc. 2019). The samples were obtained from 50 presumed Chinook salmon sampled primarily in the Strait of Georgia, identified as potential Chinook-Coho hybrids by the presence of anomalous microsatellite genotypes.

Thermo Fisher Scientific Inc. (2019). Pub. o. Rev. A.0. Life Technologies Corporation. 200 Oyster Point Blvd. South San Francisco, CA 94080. USA.

Usage Notes

The abbreviations used in the results denote: Ab=Absent; He=Heterozygous; NC=No Call.