Role of genetic markers in fisheries and aquaculture: useful tools or stamp collecting?

Abstract

We comment on the role of genetic markers in fisheries and aquaculture with a view to the future. Our goal is to encourage researchers to evaluate the molecular markers they need to deploy and shift their thinking away from analyses of stock structure towards more aggressive pursuit of questions related to genome structure and function. Examples illustrate that no one marker type is appropriate for all applications. Choice should be based on the evolutionary genetic attributes of both the species and the marker loci themselves. We evaluate three relatively new marker types: mitochondrial DNA (mtDNA) sequences, randomly amplified polymorphic DNA, and hypervariable nuclear loci. We conclude that (i) sequences of mtDNA do not necessarily detect greater polymorphism than restriction endonuclease analysis, (ii) the technical ease of randomly amplified polymorphic DNA is offset by questionable repeatability, and (iii) simulations illustrate that even new marker systems with large numbers of alleles need not detect differences among closely related yet significantly differentiated populations. Increasing the number of alleles per locus did not increase the probability of detecting significant differences. Finally, we consider the roles of genetic markers in helping to determine family relationships in pooled lots of fishes and locate genes that control an organism's phenotype (quantitative trait loci). We discuss how knowledge of quantitative trait loci can help us to understand the basis of individual differences in performance.