PCR-RFLP
Definition
PCR followed by restriction fragment length polymorphism analysis. A restriction enzyme cuts the amplicon at species-specific recognition sites; the resulting fragment pattern on a gel identifies the species. Rapid and cheap for known species pairs (e.g., cattle vs horse) but requires prior knowledge of the restriction site distribution.
- Method
- PCR amplification followed by restriction fragment length polymorphism analysis
- Mechanism
- Restriction enzyme cuts the amplicon at species-specific recognition sites
- Speed and cost
- Rapid and cheap for known species pairs
- Limitation
- Requires prior knowledge of the restriction site distribution
- Example use
- Distinguishing cattle from horse tissue
Common questions
Why does PCR-RFLP need prior knowledge of restriction sites when barcoding methods do not?+
PCR-RFLP identifies species by the fragment pattern a chosen enzyme produces, so the analyst must already know where that enzyme cuts in each candidate species' sequence to interpret the pattern. DNA barcoding instead sequences the region directly and compares it to a reference database, so it needs no pre-existing knowledge of cut sites.
When would a lab choose PCR-RFLP over full sequencing for species identification?+
When the candidate species are already known and limited in number, such as confirming meat species in a food-fraud case, PCR-RFLP is faster and cheaper per sample than sequencing, making it practical for routine screening rather than open-ended identification.
Related terms
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- BOLD Systems
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- COI (COX1)
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- Cytochrome B (Cyt B)
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- ITS Region
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- SILVA
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