RAPD - (Oct/12/2005 )
WHAT THE IMPORTANCE OF RAPD AND PCR IN POPULATION STUDY?
What is RAPD?
RAPD= Random Amplification Polymorphic DNA
You design two arbitrary "multi-locus" primers (usually 10 nucleotides long) to amplify unknown (random) segments of DNA using a common PCR reaction. In this way, you obtain different patterns of bands for individuals in a population, because of polymorphisms.
It has some pros:
it allows you to make an amplification even if your genome is not sequenced,
it's fast and not labor intensive.
but also some cons:
they are dominant (you can see for every locus the presence/absence of a band, but you can't discriminate between heterozygote a/- and homozygote a/a)
this kind of analysis is not very reproducible.
Here's an article, that would explain you everything better:
http://www.pubmedcentral.nih.gov/articlere...ubmedid=1979162
Hope this helps!!!
Cheers!
WHAT THE IMPORTANCE OF RAPD AND PCR IN POPULATION STUDY?
What is RAPD?
RAPD is stand for randomly amplified polymorphic DNAs.
RAPD stand for Randomly amplified polymorphic DNAs
this can be used to study the population diversity and we can refine the RAPD marker to a SCAR ((sequence characterized amplified regions) marker if we have positive and reproducible results from RAPD and they are useful for our study in apopulation.
in general, RAPD uses a decamer as a primer and it will amplify the sequences that are inbetween the inverse repeats of the primer as we use only single primer for RAPD.
RAPD-PCR is cheap and fast, and it has has a good discriminatory power, but reproducibility is very poor.
The primers used are very sort (normaly 10 mers), and additionaly, mismatches are supossed to happen. Those mismatches are very sensitive to experimental conditions, and although good reproducibility has been reported in a few cases, the reproducibility reported has been mostly within a laboratory. Comparison between laboratories has shown poor reproducibility. Consecuentely, Most users will use RAPD-PCR to compare strains within a unique experiment (bands pattern in different gels are not compared).
I compared about 2-3 years ago results reported in the literature for RAPD-PCR in sequenced bacteria with theoretical results we were supossed to get in silico (try http://insilico.ehu.es/PCR to simulate PCR experiments against bacterial genomes), and we were unable to detect common bands between wet and insilico experiments. We tried our own experiment with a sequenced bacteria (Salmonella Typhimurium LT2) with primers selected by using computational methods, and we were uneble to match the results.
In my experience, in case you have a few strands you want to compare (maximum will be the number of sample to be loaded in a gel), you may use RAPD-PCR as a powerful tool. In case number of strands is higher, try a different technique.
RAPD is pretty old technique for DNA polymorphisms analysis
Although it easy and less expensive to perform, but the unstable result make RAPD less used today.
I’ve used RAPD for molecular marker sreening 10 years ago and with bad memory, for I always lost marker band found previously and turn to think that RAPD is unbelievable…
After years I found that RAPD, in fact is more sensitive to PCR reaction condition. If you hope get stable results, you’d better use the same condition all times, such as use the same brand Taq… I learned that students in some labs use the exact same Taq and buffer for whole research works, and their results is more reproducible and believable than other labs, although you might not repeat their result at your lab since you might not use the same PCR condition. Now I found such old technique still be used by scientists in US for marker screening. They could reproduce their results obtained several years ago. While, they might still get trouble if let them change to different brand of Taq…
Unlike molecular maker screening, you could not use SCAR marker in POPULATION STUDY, so what you should do is keeping your PCR condition as same as possible…