Use of PCR-RFLP assays to detect genetic variation at single-copy nuclear loci in striped bass (Morone saxatilis).

We developed three assays that detect genetic variation at single-copy nuclear loci in striped bass (Morone saxatilis). Because these assays are based on restriction enzyme digests of DNA amplified by the polymerase chain reaction (PCR-RFLP), they are easy to perform on large numbers of samples. Breeding trials demonstrated that the alleles identified in each of the three assays are inherited in a Mendelian fashion as codominant alleles at single-copy loci. To demonstrate the utility of these PCR-RFLP assays, we compared the genetic composition of striped bass populations from the Congaree River in South Carolina and from the Choptank River in Maryland. Allele frequencies were significantly different at the SB14 locus, suggesting that the two populations may be genetically distinct. Furthermore, during the development of the PCR-RFLP assays, we demonstrated that the GT(n) microsatellite-associated DNA regions (MSA regions) contained RFLPs at a frequency 9-fold higher than that observed for randomly chosen segments of DNA. If MSA regions proved to be variable in other organisms as well, they could provide a valuable source of intraspecific variation.