RAPID ANALYSIS OF GENETIC-VARIATION IN ATLANTIC SALMON (SALMO-SALAR) BY PCR MULTIPLEXING OF DINUCLEOTIDE AND TETRANUCLEOTIDE MICROSATELLITES

We have isolated four microsatellites from Atlantic salmon (Salmo sala r), including three tetranucleotide loci. This class of microsatellite s exhibits a minimum of stuttering upon polymerase chain reaction ampl ification and size fractionation by denaturing polyacrylamide electrop horesis. All four loci can be co-amplified (multiplexed) in the same r eaction and exhibit nonoverlapping allele length distributions. Allele sizes for the tetranucleotide loci were determined using allelic ladd er standards (combined amplified products from several individuals), t hus improving ease and accuracy of typing alleles at these loci. To ev aluate the utility of this system for rapid assessment of population d ifferentiation, genetic variation in Atlantic salmon populations was s urveyed in three rivers from Nova Scotia, Canada. Significant differen ces in allele frequencies were observed between all populations survey ed. Heterozygosity levels at the tetranucleotide loci (>87%) were amon g the highest reported for any locus from the salmonids. The combined probability of match value for all four loci was approximately 3.4 x 1 0(-5). Given the accuracy of scoring alleles and combined information content, this multiplexed microsatellite system is ideal for parentage and familial identification and suitable for the assessment of popula tion differentiation of Atlantic salmon.