Analysis of VNTR loci in fish genomes using synthetic oligodeoxyribonucleotide probes

Abstract

A set of synthetic oligodeoxyribonucleotide (oligo) probes, OAT18, OMS1 and OAT24 carrying the (TGG)₆, (GGAT)₄ and (GACA)₆ repeat motifs, respectively, was used to analyze the variable number tandem repeat (VNTR) loci in the genomes of Oncorhyncus mykiss (rainbow trout; family Salmonidae), Oreochromis mossambicus and Oreochromis niloticus (both tilapia belonging to family Cichlidae). Of all the oligos and enzymes (AluI, MboI, HaeIII and HinfI) used, the OAT18/HaeIII combination was found to be most informative for detecting DNA fingerprinting in rainbow trout, while the OMS1/MboI combination gave the most informative pattern for the Or. niloticus genome. In the rainbow trout genome, all three repeat loci were hypervariable, revealing varying degrees of polymorphism as compared to tilapia genomes. Startlingly, the OAT24 probe did not cross-hybridize with Or. mossambicus and lamprey salmon (Lampetra japonica) although GACA repeats have been reported to be evolutionarily conserved in all eukaryotes studied thus far. Cluster analysis with respect to GGAT repeat loci revealed that Or. niloticus diverged from Or. mossambicus before the separation of On. mykiss, suggesting the relatively recent evolution of these loci in rainbow trout, compared to the tilapia genomes. These highly informative probes will find application in various genetic studies of fishes.