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SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus)

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Abstract

The ability to identify sex is necessary in population biology for a proper understanding of the dynamics of a population. In Atlantic halibut, phenotypic sex identification is not possible due to the lack of significant external morphological differences. We developed an Illumina SNP panel for Atlantic halibut with 4000 SNPs spread evenly throughout the genome with a minor allele frequency MAF ≥ 0.4, except for N = 249 SNPs located in a sex-determining region on chromosome 12, N = 176 of these SNPs were selected to genetically identify male and female individuals using a DAPC analysis. The genomic identification of sex allows for non-lethal sex determination and validation of sex identification in the field. The SNP panel is a new genomic resource for Atlantic halibut that will make it possible to generate the genotypic data for the large number of individuals needed to estimate population abundance using genomics and the Close Kin Mark Recapture (CKMR) approach, an emerging component of fisheries management and stock monitoring.

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Data Availability

Data analyzed in this study will be made available in GenBank (NCBI) and scripts related to data analysis will be uploaded to GitHub at https://github.com/weiseell/ForTheHalibut, both at acceptance for publication.

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Acknowledgements

We thank Danni Harper of DFO, Albert Moore and Dylan Buchanan of Javitech Inc., and the vast number of fisheries observers who contributed and continue to contribute to the sample collection required for this project.

Funding

This research (microarray development and manufacture) was funded by a grant from Fisheries and Oceans Canada (DFO) program: Sustainable Fisheries Science Fund (SFSF) for a project entitled: “Genomics and the estimation of population abundance in Atlantic halibut (Hippoglossus hippoglossus) using the ‘Close Kin Mark Recapture’ framework.” Funding for genotyping comes from the Government of Canada and the province of Newfoundland and Labrador’s joint Atlantic Fisheries Fund’s support of the Centre for Fisheries Ecosystems Research (Fisheries and Marine Institute of Memorial University of Newfoundland) the objectives of which are to develop new and improved groundfish stock assessment models and methods. The study is part of EMWs PhD research. EMW is funded by the Fisheries and Oceans grant, a Nova Scotia graduate student scholarship and Dalhousie University funds and a Natural Sciences and Engineering Research Council of Canada Discovery grant to DER. We acknowledge NSERC Discovery Grants to DER and JMF.

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Authors and Affiliations

  1. Department of Biology, Dalhousie University, 1355 Oxford St, B3H 4R2, Halifax, NS, Canada

    Ellen M. Weise, Mallory Van Wyngaarden, Anthony L. Einfeldt & Daniel E. Ruzzante

  2. Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, B2Y 4A2, Dartmouth, NS, Canada

    Cornelia Den Heyer & Tony Kess

  3. Department of Mathematics & Statistics, Dalhousie University, 6316 Coburg Rd, B3H 4R2, Halifax, NS, Canada

    Joanna Mills Flemming

  4. Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, 155 Ridge Rd, A1C 5R3, St. John’s, NL, Canada

    Jonathan A. D. Fisher

  5. Population Health Research Institute, 237 Barton Street, East Hamilton, ON, L8L 2X2, Canada

    Reina Ditta & Guillaume Pare

  6. Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada

    Mallory Van Wyngaarden

  7. Parks Canada, East Kootenay, BC, Canada

    Anthony L. Einfeldt

Authors
  1. Ellen M. Weise
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  2. Mallory Van Wyngaarden
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  3. Cornelia Den Heyer
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  4. Joanna Mills Flemming
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  5. Tony Kess
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  6. Anthony L. Einfeldt
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  7. Jonathan A. D. Fisher
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  8. Reina Ditta
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  9. Guillaume Pare
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  10. Daniel E. Ruzzante
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Contributions

The microarray was designed by Mallory Van Wyngaarden, Tony Kess, Anthony L. Einfeldt, and Daniel E. Ruzzante. Ellen M. Weise, Mallory Van Wyngaarden, Tony Kess, and Anthony L. Einfeldt performed the analysis. Daniel E. Ruzzante, Cornelia Den Heyer, Joanna Mills Flemming, and Jonathan Fisher designed the CKMR project and Reina Ditta and Guillaume Pare contributed new tools. Ellen M. Weise, Mallory Van Wyngaarden, and Daniel E. Ruzzante wrote the initial draft. All authors commented and edited the paper.

Corresponding authors

Correspondence to Ellen M. Weise or Daniel E. Ruzzante.

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Weise, E.M., Van Wyngaarden, M., Den Heyer, C. et al. SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus). Mar Biotechnol 25, 580–587 (2023). https://doi.org/10.1007/s10126-023-10227-2

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  • DOI: https://doi.org/10.1007/s10126-023-10227-2

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