Skip to content

Research at St Andrews

A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon

Research output: Contribution to journalArticle

Abstract

Accurate parentage assignment is key for the development of a successful breeding program, allowing pedigree reconstruction from mixed families and control of inbreeding. In the present study we developed a workflow for the design of an efficient single nucleotide polymorphism (SNP) panel for paternity assignment and validated it in Atlantic salmon (Salmo salar L.). A total of 86,468 SNPs were identified from Restriction Site Associated DNA Sequencing (RAD-seq) libraries, and reduced to 1517 following the application of quality control filters and stringent selection criteria. A subsample of SNPs were chosen for the design of high-throughput SNP assays and a training set of known parents and offspring was then used to achieve further filtering. A panel comprising 94 SNPs balanced across the salmon genome were identified, providing 100% assignment accuracy in known pedigrees. Additionally, the panel was able to assign individuals to one of three farmed salmon populations used in this study with 100% accuracy. We conclude that the workflow described is suitable for the design of cost effective parentage assignment and traceability tools for aquaculture species.
Close

Details

Original languageEnglish
Pages (from-to)59-64
Number of pages6
JournalAquaculture
Volume476
Early online date4 Apr 2017
DOIs
StatePublished - 1 Jul 2017

    Research areas

  • SNP, Parentage assignment, Atlantic salmon, Traceability, Pedigree, Workflow

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Characterization of the transcriptome of fast and slow muscle myotomal fibres in the pacu (Piaractus mesopotamicus)

    Mareco, E. A., Garcia de la Serrana Castillo, D., Johnston, I. A. & Dal-Pai-Silva, M. 14 Mar 2015 In : BMC Genomics. 16, 13 p., 182

    Research output: Contribution to journalArticle

Related by journal

  1. Aquaculture (Journal)

    James, M. A. (Reviewer)
    2014

    Activity: Publication peer-review and editorial workPeer review of manuscripts

Related by journal

  1. Is Europe ready for integrated multi-trophic aquaculture? A survey on the perspectives of European farmers and scientists with IMTA experience

    Kleitou, P., Kletou, D. & David, J. 1 Mar 2018 In : Aquaculture. 490, p. 136-148

    Research output: Contribution to journalArticle

  2. Effect of temperature on biochemical and cellular properties of captive Limulus polyphemus

    Coates, C. J., Bradford, E. L., Krome, C. A. & Nairn, J. 7 Mar 2012 In : Aquaculture. 334, p. 30-38 9 p.

    Research output: Contribution to journalArticle

  3. Feasibility of intertidal bottom culture of the penshell Atrina maura in Bahia Magdalena, Baja California Sur, Mexico

    Mendo, T., Koch, V., Wolff, M., Sínsel, F. & Ruiz-Verdugo, C. 4 Apr 2011 In : Aquaculture. 314, 1-4, p. 252-260 9 p.

    Research output: Contribution to journalArticle

  4. Development of a semi-closed aquaculture system for monitoring of individual amphioxus (Branchiostoma lanceolatum), with high survivorship

    Somorjai, I. M. L., Camasses, A., Rivière, B. & Escrivà, H. 2008 In : Aquaculture. 281, 1-4, p. 145-150

    Research output: Contribution to journalArticle

ID: 249576748