I am beginning to design primers for a Genotyping By Sequencing (GBS, formally RAD-tag) for two different plant population genetics studies. Can anyone share their experience with this?
GBS is a protocol to collect sequence data from a reduced representation of a genome. I wouldn't say it was "formally RAD-seq". In fact GBS has been overtaken by newer varied flavours of RAD-seq. Neither of these approaches use primers, instead they use restriction enzymes.
This response is quite late, but it seems that there are PCR primer oligos that are used in the procedure. It is these oligos that I am curious about. It seems that the common oligos that are used are derived from animals. I am curious if this the recommended oligos are also suitable for plants. The oligos are part of the first process to anneal the adapters prior to ligation.