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Dear Colleague, here are only two examples (there are many!) where you can see that you can get quite easily good results with PCR primer designed for SSR motives (i.e. GATCGATCGATCGATC) Many of these primers should also work in your new species.

Thanks Frank Dunemann for your kind and informative response.

Different concentrations of genomic DNA (5, 10, 20, and 40 ng), primers (5, 10 and 20 pmol) and Taq DNA polymerase (0.3, 0.5, 0.6, 0.8U) can be tested in various combinations to determine the most suitable concentration for obtaining good and analyzable amplification products. Preliminary screening experiments can be set up using 25 primers either from RAPD or ISSR and assayed with the extracted DNA sample to screen out the primers that generated highly reproducible bands. Once the optimal PCR conditions for each primer is established successfully, final PCR reactions with the selected primers can be carried out to assess the genetic variation or fidelity studies based on the experimental objectives/needs.

Can this article help you get the answer.

See the literature first to find out which issr primers have been used previously for the particular plant or plant belonging to same genus. Primers sequences are available and you can screen around 25 different primers and select those which produce reproducible, clear and scorable bands. Some may not produce bands or not generate reproducible bands.