Clone identification

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One of the greatest difficulty in the maintenance of a living
collection of conspecific perennial plants over a long period of time
is to ascertain the genetical continuity of the original individual,
i.e. successive generations are all part of the same clone.

Does such a thing as a simple, cheap and quick molecular method to
check that exist ?   It would be applied on a large grass collection.
The idea is to use the data as a qualitative fingerprint.  No need
for a thorough identification of the compounds involved.

I would appreciate pragmatic comments from those peoples
dealing with such problem.

Thanks a lot.