LAUSR

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.