Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene
| Main Authors: | Von Bargen, Jennifer, Smith, Christian T., Rueth, John |
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| Format: | info dataset Journal |
| Terbitan: |
, 2015
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4977004 |
Daftar Isi:
- Genotypic sex identification assays can provide valuable information about fish populations when phenotypic sex determination is difficult. Here we describe the development of a TaqMan® assay (Ots_SexID) designed to identify the genotypic sex of Winter-Run Chinook salmon collected from the Sacramento River and spawned at the Livingston Stone National Fish Hatchery. The TaqMan® assay targets a region previously examined in the growth hormone pseudogene. Accuracy of the marker was assessed by comparing genotypic sex assignments for Chinook salmon spawned at Livingston Stone National Fish hatchery in 2012 (n = 84) to phenotypic sex recorded during spawning. Genotypic sex was observed to be concordant with phenotypic sex identified using Ots_SexID in 83/84 individuals, suggesting that the assay could be used to predict phenotypic sex with ~99% accuracy. To evaluate the utility of the TaqMan® assay in other parts of the species' range, we examined collections from 29 other populations ranging from Alaska to California. Sex assignments based on the assay were generally concordant with observed phenotypes, but there were some strong exceptions. These results suggest that the new assay will be very useful in Sacramento River Winter-Run Chinook salmon, but also highlight the importance of thoroughly testing any sex identification assay prior to application in a population of interest.
- Table S1Phenotypic and genotypic sex assignment of Winter-Run Chinook salmon (Oncorhynchus tshawytscha) spawned at Livingston Stone National Fish Hatchery in 2012. Phenotypic sex assignment was made during spawning. Genotypic sex assignments were made using a fragment-based assay and also using the novel TaqMan® assay, Ots_SexID. Samples for which phenotypic and genotypic sex assignment conflicted are indicated in bold font.Reference S1Baumsteiger, JD, Niemela KS, Null RE, Ardren WR. 2005. The Inclusion of Sexually-Determinate Molecular Markers into the Broodstock Selection Protocol for Winter-Run Chinook salmon at Livingston Stone National Fish Hatchery. AFTC Report.Baumsteiger et al. 2005.pdfReference S2Von Bargen J, Smith CT. 2013. Genetic identification of endangered winter-run Chinook salmon in the Sacramento River, CA, AFTC Final Report FY2012.LSNFH FY2012 Final Report.pdf