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Development of EST-SSR PCR primers within three North Pacific rockfishes of the genus Sebastes

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Abstract

Severe declines in abundance of Pacific Ocean Perch (Sebastes alutus) and other rockfishes have led to catch restrictions along the US west coast. The stock structure of many important commercial members of Sebastes spp remains a major source of uncertainty in stock assessment models. Here we report development of PCR primer pairs from 13 novel EST-SSR loci obtained from public Sebastes EST databases, and redesigned primer pairs from six published EST-SSR loci. Amplification and diversity data from these and 27 published EST-SSR loci are reported for S. polyspinis, S. alutus, and two cryptic sub-types of S. aleutianus. Loci were moderately polymorphic, with heterozygosities averaging 0.44, and allele number averaging 5.2 across all loci and species. Divergence between the two S. aleutianus sub-types was high (mean F ST = 0.33) allowing for unambiguous identification. The loci will be informative for resolving stock structure issues and possible local adaptation along the species’ ranges.

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Acknowledgments

Samples provided by J. Hyde, C. Kimbrell, and E. Lynn at Southwest Fisheries Science Center, La Jolla, CA. Funding provided by NPRB grant #1109. NPRB publication 359.

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Authors and Affiliations

  1. Juniata College, 1700 Moore St., Huntingdon, PA, 16652, USA

    Vincent P. Buonaccorsi & Brittani Raybuck

Authors
  1. Vincent P. Buonaccorsi
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  2. Brittani Raybuck
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Corresponding author

Correspondence to Vincent P. Buonaccorsi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

12686_2012_9742_MOESM1_ESM.pdf

Supplementary material 1 (PDF 259 kb). Online Resource A. Metadata associated with samples. Sample ID from lead author’s lab, tray and vial number from NMFS laboratory where tissue samples are stored, general location of catch, NOAA vessel, trip number, set number, genus and species identification, date of capture, species location of capture, miscellaneous comments, NMFS DNA extraction ID, sex, total length and weight are shown

Supplementary material 2 (PDF 281 kb). Online Resource B. Allele frequencies and counts by locus and species

Supplementary material 3 (PDF 261 kb). Online Resource C. Allele size range by locus and species

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Buonaccorsi, V.P., Raybuck, B. Development of EST-SSR PCR primers within three North Pacific rockfishes of the genus Sebastes . Conservation Genet Resour 5, 97–103 (2013). https://doi.org/10.1007/s12686-012-9742-2

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  • DOI: https://doi.org/10.1007/s12686-012-9742-2

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