Random Amplified Polymorphic DNA (RAPD marker) Amplify genomic DNA randomly between two identical short sequence with single short oligonucleotide primer (10 base pair) based on PCR amplification by using low annealing temperature (35 to 45 degree Celsius) to increase sequence amplification without exactly complementary to primer sequence therefore changes in DNA sequence at each locus in RAPD marker assess by presence (1) or absence (0) bands on gel Hence RAPD polymorphism occur due to base substitution at primer binding sites or indels in regions between binding sites and the mismatch between primer and DNA template results decrease amount of PCR product, Initial denaturation start at 94 degree Celsius for 10 minutes and denaturation temperature should be at 94 degree Celsius for 1 minute and annealing temperature should be at 37 to 45 degree Celsius for1 minute and extension temperature should be at 72 degree Celsius for 1 minute and final extension should be at 72 degree Celsius for 10 minutes and cooling temperature should be at 4 degree Celsius forever, Polymorphic band must be clone and make sequence to design new primers to amplify specifically, RAPD marker provide quick screen of DNA sequence without require any previous sequence information by using small amount of DNA to get high polymorphism therefore RAPD marker classify as simple and rapid and cheap marker, RAPD marker classify as a dominant marker inheritance because homozygous and heterozygous states can not be differentiate on gel and not locus specific because short primer can amplify any of random sequence in genome and it's bands are very sensitive to reaction conditions and DNA quality and PCR temperature so RAPD marker Poor Reproducibly and sensitive, RAPD marker use in genetic diversity studies and germplasm characterization and genetic structure of population and genome mapping, RAPD marker is a PCR based technique in which single short oligo-nucleotide primer use to amplify random sequences from DNA template and it's product separate by horizontal electrophoresis and visualize by ultraviolet illuminate of ethidium bromide stained agarose gel so polymorphism of amplified sequence corresponds to genetic differences (Watch Related Video in #geneticteacher) #geneticteacher

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