RAPD-PCR

Definition

Random Amplified Polymorphic DNA PCR; a PCR-based molecular fingerprinting technique that uses short, arbitrary primers (typically 10–12 nucleotides) to amplify anonymous genomic regions without prior sequence knowledge. The primers anneal at multiple partially complementary sites throughout the genome; when sites occur in opposite orientation within amplifiable distance, the intervening DNA is amplified and visualized as banding patterns on agarose gels. RAPD-PCR generates simple genomic fingerprints useful for detecting genetic variation, discriminating strains or populations, and constructing rough genetic maps.

Etymology

Acronym from Random Amplified Polymorphic DNA – Polymerase Chain Reaction; pronounced "rapid" for convenience

Example

RAPD-PCR has been used to distinguish cryptic species of bark beetles (Scolytinae) and to assess gene flow among fragmented populations of wolf spiders (Lycosidae) without requiring species-specific primer design.

Synonyms

• RAPD
• arbitrarily primed PCR

Related Terms

• DNA barcoding
• microsatellite
• genetic fingerprinting
• population genetics
• molecular ecology
• AP-PCR
• DAF

Usage Notes

RAPD-PCR is technically simple and requires minimal DNA, but it has lower reproducibility than targeted marker systems due to sensitivity to reaction conditions and primer-template mismatches. Results are typically dominant (presence/absence) rather than codominant, limiting heterozygote detection. The technique has been largely superseded by more robust methods (AFLP, microsatellites, SNP genotyping) in many applications, though it remains useful for rapid screening when no sequence data exist. Not to be confused with taxon names in the moth genus Rapdalus.