Question

Which one of the following is not a PCR based molecular marker?
A. RAPD
B. AP-PCR
C. DAF
D. RFLP

Answer 1

A molecular marker is a sequence of DNA that is easily identified. These sequences are present at specific locations of the genome. Molecular markers are used to identify differences of base pairs at a specific location (also called polymorphisms) in an unknown pool of DNA. Molecular markers can be of two types – PCR based and DNA hybridization based.

Complete answer:
Option (a) is incorrect. Random Amplification of Polymorphic DNA or RAPD is a PCR based molecular marker. Short random primers of 8 to 10 base pairs are created and the PCR is performed. The primers adhere to specific sequences throughout the genome. the knowledge of DNA sequence of the target organism is not required. RAPD helps to compare the DNA of two organisms or of an organism whose DNA has previously not been sequenced. RAPD can be used to trace, study phylogenetic relationships.

Option (b) is incorrect. AP-PCR is Arbitrarily Primed PCR. It is a type of DNA Fingerprinting that uses random primers. The fingerprint obtained by this process helps to compare the genome of closely related individuals. AP-PCR can be used to detect somatic mutations, polymorphisms in DNA and taxonomical studies.

Option (c) is incorrect. DAF is DNA Amplification Fingerprinting. It is a PCR based approach to identify polymorphisms in DNA. This process utilizes short primers that adhere to specific sequences upon amplification. The amplified products are then subjected to PAGE or Polyacrylamide Gel Electrophoresis. The result of this procedure is short fingerprints of a very large range.

Option (d) is correct. Restriction Fragment Length Polymorphism or RFLP is a non-PCR based approach. The RFLP analysis differentiates or compares individuals based on polymorphisms in their genome. These polymorphisms are detected by restriction digestion and the subsequent comparison of the lengths of the restriction fragments. RFLP is the first DNA profiling method to be adapted by the scientific community. It was widely used for paternity testing and identification of genetic disease markers.

Hence, the correct answer is option (D).

Note: Molecular markers help to identify polymorphisms in DNA. Markers are a part of one’s genome and are used as landmarks in analysis of a genome. There are several ways to identify a molecular marker. RFLP analysis is one such PCR independent method of molecular marker identification. It uses restriction enzymes to cut a DNA and produce restriction fragments which are then compared for analysis. Other methods are PCR based like DAF, AP-PCR and RAPD.