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

Citation
Mj. Bagley et al., Choice of methodology for assessing genetic impacts of environmental stressors: Polymorphism and reproducibility of RAPD and AFLP fingerprints, ECOTOXICOL, 10(4), 2001, pp. 239-244
Citations number
23
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Environment/Ecology
Journal title
ECOTOXICOLOGY
ISSN journal
0963-9292 → ACNP
Volume
10
Issue
4
Year of publication
2001
Pages
239 - 244
Database
ISI
SICI code
0963-9292(2001)10:4<239:COMFAG>2.0.ZU;2-K
Abstract
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.