Choice of methodology for assessing genetic impacts of environmental stressors: Polymorphism and reproducibility of RAPD and AFLP fingerprints

PCR-based multi-locus DNA fingerprints represent one of the most informativ e and cost-effective measures of genetic diversity and are useful populatio n-level biomarkers of toxicologic and other anthropogenic impacts. However, concerns about reproducibility of DNA fingerprints have limited their wide r use in environmental biology. We assessed polymorphism and reproducibilit y of two common fingerprinting techniques, RAPD (randomly amplified polymor phic DNA) and AFLP (amplified fragment length polymorphism), in pedigreed p opulations of rainbow trout (Oncorhynchus mykiss) to derive general rules f or selective removal of problematic fingerprint bands. We found that by exc luding bands that comprised less than 1% of total intensity, and by excludi ng the largest and smallest 10% of the bands, we could achieve nearly 100% reproducibility of AFLP fingerprints. Similar application of band exclusion criteria to RAPD fingerprints did not significantly enhance their reproduc ibility, and at least 15% of RAPD bands were not fully repeatable, heritabl e, or transmittable. The RAPD technique produced more polymorphic fingerpri nts than AFLP; however, considering that a substantial proportion of RAPD m arkers did not demonstrate Mendelian inheritance patterns, the AFLP methodo logy is to be preferred for future research.