The aquaculture of Atlantic salmon began in Australia in the mid-1960' s with an importation of ova from Canada to New South Wales. Anecdotal evidence suggested that the Australian population went through a severe bottleneck event during the early years due to poor survival and subsequent small broodstock numbers. The population, however, survived and numbers increased such that a few hundred broodstock were available each year from the early 1970' s. The now flourishing Tasmanian Atlantic salmon indust1y was founded from the New South Wales population in the mid 1980's. About 115 000, 180 000 and 275 000 ova were brought to Tasmania in 1984, 1985 and 1986, respectively. The Tasmanian industry now produces over 7 000 tonnes annually, with the majority of smolt being supplied by the Salmon Enterprises of Tasmania Pty Ltd (SAL TAS) commercial hatchery. SALT AS has for the past ten years maintained the Tasmanian broodstock, using several hundred females and males from two-year classes to produce each year's supply of smolt.

An important task for hatchery managers is the maintenance of genetic variation in their broodstock, and molecular geneticists can accurately assess genetic variation and detect meaningful changes. In recent years a new class of DNA marker - microsatellites - has shown promise for studies of genetic variation, progeny testing, genome mapping and quantitative trait loci (trait markers). We constructed an Atlantic salmon genomic DNA library which contains over 9 000 clones and several hundred potential microsatellite DNA markers. The DNA sequences of 24 of these have been determined and primers developed for eight markers for use in genetic studies. Three of these, plus five obtained from overseas contacts, were used to examine genetic variation in the Tasmanian population. As these markers were applied to the same individual fish that had earlier been examined for allozyme and mitochondrial DNA (mtDNA) variation, the relative abilities of these three techniques to detect genetic changes in hatchery populations could be assessed.

The genetic variation present in the Tasmanian and Canadian populations in 1993 was compared using these three molecular genetic methods - allozymes, mitochondrial DNA and nuclear DNA microsatellites. Some small but statistically significant allele frequency differences between the two populations were observed for one of seven polymorphic allozyme loci and for mitochondrial DNA haplotypes. However, there was no evidence of reduced genetic variability in the Tasmanian population. There were small but significant allele frequency differences observed at four of the eight microsatellite loci, and this analysis did show evidence of a small overall loss of genetic variation (loss of alleles and heterozygosity) in the Tasmanian population.

To investigate this suggested loss of genetic variation, and whether this occurred since the introduction to Tasmania or, as anecdotally suggested, during the early years of domestication in New South Wales, the genetic variation (microsatellites and allozymes) present in the Tasmanian and New South Wales populations in 1997 was then compared with that in the two previous samples.