What is RAD-Seq?
Restriction site associated DNA sequencing (RAD-Seq) using the Illumina technology was initially published in PLoS One and in PLoS Genetics. Along with other studies, these studies demonstrated that this smart technique can be very useful for the identification and further analysis of a high number of genetic markers distributed over the genome. This is especially advantageous if working with non-model organisms where no reference sequence is available. Briefly, RAD-Seq results in a reduced representation of the respective genome, because only fragments near a specific type of restriction site are sequenced to deep coverage. Such fragments are called ‘RAD tags’ and serve in subsequent analysis steps as a reference for the design of genetic markers. The overall number of possible RAD tags within an organism strongly depends on the restriction enzyme of choice and the genome of interest.