If you are characterizing local diversity of F. vesca genome, do AFLP that is the best.. Because it amplifies several loci in a single go. The genome sequence of F. vesca is already available and I suppose one can design AFLP primers for that. or secondly you can down load the sequences of F. vesca chromosome wise and feed them to the BATCHPrimer3 a primer designing software. You can screen out for the presence of SSRs and simultaneously you can also generate primers against it. So you can randomly select designed SSR markers from all the 7 chromosome and do the chaacterization. Look I have done some work for you enclosed in attached file
Unfortunately I'm working in a small lab with low budget, so I do not have enough equipment for AFLP. Developing new SSR also be costly. I need a core set but i can't found something similar. But i found this publications newly.
I guess, i'm select ssrs in this study.
Article Simple Sequence Repeat Marker Development and Mapping Target...