PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics

This paper outlines a PCR-based approach for population genetics thatoffers several advantages over conventional Southern blotting methods forrevealing restriction-fragment-length polymorphisms (RFLPs) in nuclear DNA.Primers are constructed from clones isolated from a nuclear DNA library,and these primers subsequently are employed in in vitro syntheses ofhomologous regions. Amplified products are then screened directly for RFLPsby using gel-staining procedures. Population applications for thisPCR-based approach, including potential strengths and weaknesses, areexemplified by two RFLP data sets generated to estimate (a) male-mediatedgene flow in the green turtle (Chelonia mydas) and (b) geographicpopulation genetic structure in the American oyster (Crassostreavirginica). Restriction assays of amplified products from 14 or 15independent primer pairs in each species revealed polymorphisms at severalloci that proved highly informative in the population genetic analyses. Ingeneral, the Mendelian polymorphisms produced by this PCR-based approachwill provide useful genetic markers for population studies, particularly insituations where simpler and less expensive allozyme methods have failed,for whatever reason, to provide adequate information.