Organization of Microsatellites Differs between Mammals and Cold-water Teleost Fishes

Abstract

Microsatellites, in particular (dG-dT)n and (dG-dA)n dinucleotide repeats, are abundant and display a high degree of length polymorphism and heterozygosity in eukaryotic genomes. Here, we report the cloning and characterization of 64 microsatellite sequences from Atlantic cod, Gadus morhua. The microsatellites were classified as perfect, imperfect, and compound repeats. The length and integrity of these repeats were compared with microsatellites characterized from two other teleosts, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar), and from three mammalian genomes, human, porcine, and canine. Differences were found in the proportions of the repeat classes; however, the most significant difference between microsatellites from teleost fishes and mammals was the propensity of the former to be of greater length: some cod and rainbow trout microsatellites were more than twice the size of the longest microsatellite repeats reported for any mammalian genome. Primers for PCR amplification were constructed for seven of the cod microsatellites. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for a sample population. Amplification with these cod primers was also carried out on a number of related gadids. These polymorphic microsatellite loci have enormous potential utility as genetic markers for use in population, breeding, and evolutionary studies.