Assessment of the level of heterozyogosity in the Tasmanian Atlantic salmon (Salmon salar) population using single nucleotide polymorphim markers

The level of heterozygosity in the Tasmanian Atlantic salmon population was investigated using SNP data from 93 fish from unselected broodstock and 2991 single nucleotide polymorphisms (SNPs). Three approaches were used as measures of the likelihood of two alleles being identical by descent: two homozygosity indices, which have not been used on SNP data before and an inbreeding coefficient for the SNP markers based on observed and expected heterozygosity. As expected, the two homozygosity indices yielded highly correlated results, because biallelic SNP markers are all equally informative. The observed and expected heterozygosity at the SNP loci were very similar and that was reflected in intermediate inbreeding coefficients. All three analysis methods indicated a moderate likelihood that alleles are identical by descent, and offspring tested came from unrelated parents. Most markers were in HardyWeinberg-equilibrium. The SNP data support previous microsatellite studies concluding that the Tasmanian Atlantic salmon population has a moderate level of genetic diversity, as indicated by homozygosity indices and the inbreeding coefficient, and that hatchery protocols over the 40 years since the population was established in Australia have maintained a genetically healthy population.