Projects per year
RESULTS: Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified.
CONCLUSIONS: We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.
- Atlantic salmon
- RAD sequencing
- Infectious pancreatic necrosis
- Single nucleotide polymorphism
- Paralogous sequence variant
Dutia, B., Archibald, A., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Collie, D., Digard, P., Freeman, T., Glass, E., Grey, F., Hocking, P., Houston, R., Hume, D., Kaiser, P., Nash, A., Sang, H., Sharp, C., Watson, M. & Whitelaw, B.
1/04/12 → 31/03/17
1/08/11 → 31/07/14