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Which of the molecular marker techniques uses a single primer in a PCR reaction for identifying polymorphisms between genotypes?

Question : Which of the molecular marker techniques uses a single primer in a PCR reaction for identifying polymorphisms between genotypes?( CSIR DECEMBER 2024)
  1. SSR ( Simple sequence repeats)
  2. AFLP (Amplified fragment length polymorphism)
  3. RAPD (Randomly amplified polymorphic DNA)
  4. SCAR (Sequence characterized amplified regions)
Answer : 3. RAPD( Randomly amplified polymorphic DNA)


RAPD (Random amplification of polymorphic DNA):  Random Amplification of Polymorphic DNA (RAPD) is a technique grounded in PCR that serves as a molecular marker to pinpoint genetic differences among various genotypes. This approach employs a single primer in a PCR reaction to detect polymorphisms by amplifying random DNA fragments dispersed throughout the genome. Random amplification of polymorphic DNA
RAPD does not require any specific knowledge of the DNA Sequence of the target organism. 
 The major limitation of the RAPD method is the reproducibility and dominant inheritance. several factors influence the reproducibility of RAPD reactions such as quality and quantity of template DNA, PCR buffer, concentration of magnesium chloride, primer to template ratio and annealing temperature. RAPD markers are dominant markers, and hence do not distinguish dominant homozygotes from heterozygotes.
RAPD MECHANISM FOR IDENTIFYING POLYMORPHIC DNA


A different pattern of amplification is observed in different sample types. Hence the RAPD can help in the polymorphism studies. 


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