Difference Between RAPD and RFLP


Main Difference

Genetic markers are genes located at known position on a chromosome that is used for identification of individuals or species. A genetic marker is a short sequence of DNA which can be described as variation that can be observed. Genetic markers are used to study connection between inherited diseases and genetic causes. RAPD (Random amplification of polymorphic DNA) and RFLP (Restriction fragment length polymorphism) are types of genetic markers. Both of them differ with each other in many aspects like: amount of DNA required in RAPD is less while in RFLP large amount of DNA is required for quantification.


Random amplification of polymorphic DNA or RAPD is a useful technique used to construct genetic map. It is PCR based method in which the segment of DNA that are amplified are random. It is a very basic method for obtaining molecular finger printing or strain species. RAPD can detect 1-10 loci. By using random primers it helps to analyze the genetic diversity of an individual. RAPD requires only single primer for amplification. RAPD does not require and particular knowledge of the DNA sequence of target individual which is unlikely to other traditional PCR methods. RAPD is an inexpensive but very useful technique. It is also faster technique, five times faster than RFLP. Method of RAPD involves: extraction of DNA followed by amplification using random primers by PCR and last gel electrophoresis of DNA that is amplified and visualization of markers. Selection of correct sequence for the primer is important because different sequence will produce different pattern and possibility of allowing more specific recognition of individual strains.



Restriction fragment length polymorphism or RFLP is a very useful technique to study genomic sequence of DNA. It is developed for mapping the chromosomes of human, maize, mice, tomato etc. RFLP is a non-PCR based method in which DNA sample is broken into fragments and then they are digested by restricting enzymes and results in restriction fragments which are separated according to their length by gel electrophoresis. In RFLP only 1-3 loci are detected. This technique was the first DNA profiling technique inexpensive enough to see widespread application. RFLP is a useful tool for the detection of genetic disorders, risk for disease and paternity testing. RFLP analysis was also useful in the identification of evidences retrieved from crime scene because it was the basis for early methods of finger printing. RFLP technique is sub-divided into two: single- (SLP) and multi locus probe (MLP) paradigms. SLP is more preferred over MLP because it is easily interpreted, sensitive and it can analyze mixed DNA sample. In SLP, we can get data even when the DNA is degraded like in bone remains.


Key Differences

  1. RAPD is a useful technique to construct DNA map while RFLP technique is useful to study genomic sequence of DNA.
  2. RAPD analysis is PCR based method while RFLP analysis is non-PCR based method.
  3. In RAPD small quantity of DNA is required while in RFLP large quantity of DNA is required.
  4. RAPD can detect 1-10 loci while RFLP can detect 1-3 loci.
  5. RAPD is five times faster than RFLP.
  6. Method of RAPD includes: DNA extraction then amplification using random primers by PCR and last gel electrophoresis of amplified DNA and visualization of markers.
  7. Method of RFLP includes: DNA sample is broken into fragments and digested by restricting enzymes and results in restriction fragments which are separated according to their length by gel electrophoresis and last southern blot by specific probes and detection of specific sequence.
Janet White

Janet White is a writer and blogger for Difference Wiki since 2015. She has a master's degree in science and medical journalism from Boston University. Apart from work, she enjoys exercising, reading, and spending time with her friends and family. Connect with her on Twitter @Janet__White

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