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A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon
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dc.contributor.author | Holman, Luke E. | |
dc.contributor.author | Garcia de la Serrana, Daniel | |
dc.contributor.author | Onoufriou, Aubrie | |
dc.contributor.author | Hillestad, Borghild | |
dc.contributor.author | Johnston, Ian A. | |
dc.date.accessioned | 2018-04-04T23:34:00Z | |
dc.date.available | 2018-04-04T23:34:00Z | |
dc.date.issued | 2017-07-01 | |
dc.identifier | 249576748 | |
dc.identifier | fa16c074-7aeb-4a91-b16a-4f7a4f0fbbe9 | |
dc.identifier | 85017680145 | |
dc.identifier | 000402466100008 | |
dc.identifier.citation | Holman , L E , Garcia de la Serrana , D , Onoufriou , A , Hillestad , B & Johnston , I A 2017 , ' A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon ' , Aquaculture , vol. 476 , pp. 59-64 . https://doi.org/10.1016/j.aquaculture.2017.04.001 | en |
dc.identifier.issn | 0044-8486 | |
dc.identifier.other | RIS: urn:95C666955EC66F5247985DEBC5234384 | |
dc.identifier.other | ORCID: /0000-0002-7796-5754/work/47136013 | |
dc.identifier.uri | https://hdl.handle.net/10023/13071 | |
dc.description | This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 654008. | en |
dc.description.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. | |
dc.format.extent | 6 | |
dc.format.extent | 1024964 | |
dc.language.iso | eng | |
dc.relation.ispartof | Aquaculture | en |
dc.subject | SNP | en |
dc.subject | Parentage assignment | en |
dc.subject | Atlantic salmon | en |
dc.subject | Traceability | en |
dc.subject | Pedigree | en |
dc.subject | Workflow | en |
dc.subject | QH301 Biology | en |
dc.subject | SH Aquaculture. Fisheries. Angling | en |
dc.subject | DAS | en |
dc.subject.lcc | QH301 | en |
dc.subject.lcc | SH | en |
dc.title | A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon | en |
dc.type | Journal article | en |
dc.contributor.sponsor | European Commission | en |
dc.contributor.institution | University of St Andrews. School of Biology | en |
dc.contributor.institution | University of St Andrews. Scottish Oceans Institute | en |
dc.contributor.institution | University of St Andrews. Marine Alliance for Science & Technology Scotland | en |
dc.contributor.institution | University of St Andrews. Centre for Research into Ecological & Environmental Modelling | en |
dc.identifier.doi | 10.1016/j.aquaculture.2017.04.001 | |
dc.description.status | Peer reviewed | en |
dc.date.embargoedUntil | 2018-04-04 | |
dc.identifier.grantnumber | 654008 | en |
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