A Linkage Map of the Atlantic Salmon (Salmo salar) Based on EST-Derived SNP mMarkers

Background: The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, thespecies displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with fullgenome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it isimportant to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundredsingle nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage mapscontaining SNP and microsatellite markers. We also investigated further the distribution of male and femalerecombination events across the genome, and estimated levels of LD between pairs of markers.Results: The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which weresuccessfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicatingthat there is little overlap between regions in which male and female crossovers occur. The female map is likely to haveclose to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regionswhere male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodalfashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence ofrecent admixture in the population, the population being a 'synthetic' breeding population with contributions fromseveral distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higherthan 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM.Conclusion: The linkage map presented here is an important resource for genetic, comparative, and physical mappingof the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the malemap length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparentlysmall physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.