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

• Published in: Aquaculture
• Main Authors: Holman, Luke E., Garcia de la Serrana, Daniel, Onoufriou, Aubrie, Hillestad, Borghild, Johnston, Ian A.
• Other Authors: European Commission, University of St Andrews. School of Biology, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Centre for Research into Ecological & Environmental Modelling
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2018
• Subjects: SNP; Parentage assignment; Atlantic salmon; Traceability; Pedigree; Workflow; QH301 Biology; SH Aquaculture. Fisheries. Angling; DAS; QH301; SH; Salmo salar
• Online Access: http://hdl.handle.net/10023/13071; https://doi.org/10.1016/j.aquaculture.2017.04.001

This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 654008. 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. Postprint Peer reviewed