Several molecular markers have been used for assessment of the genetic stability of micropropagated plants (RAPD, AFLP, ISSR among others). Since generally you are not expecting great differences between the propagated plants and the mother plant, I think the most important feature for the marker of choice would be a high polymorphism. AFLP is highly polymorphic, but the cost is higher and more labor-intensive than RAPD or ISSR.
Whatever marker you choose, I recommend including a comparison of the genetic variability of seed-propagated plants (where you would expect more differences). In that way, if you don't see differences in your micropropagated plants, you can be sure it is due to genetic fidelity, not because of a low discriminating power of the marker.
SSR (microsatellite markers) are among the best choice for studying genetic diversity. Ofcourse AFLP is highly polymorphic but same as Gustavo said it is costly and labor intensive.
@Vishwanath K., you might be confusing AFLP with RAPD, because as far as I know, AFLP are quite reproducible, which is not the case for RAPD...
SSR are definitely an excellent choice, but you need some information about the presence of these repeat sequences in your species (if they are di, tri-nucleotide repeats, sequence of the repeats). The microsatellites developed for one species can not always be applied to another species, especially if it is not closely related. So, if microsatellites are already developed for your species of interest, definitely go for it... otherwise, you'll have to try markers where no previous knowledge of the genome is needed (like ISSR, AFLP, RAPD, etc...)
Dear Gustav You are right..........
http://documents.plant.wur.nl/pri/products/biodiv/15.pdf
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