DArT works by reducing the complexity of a DNA sample to obtain a ‘representation’ of that sample. Our preferred method of complexity reduction relies on a combination of restriction enzyme digestion and adapter ligation, followed by amplification (Wenzl et al., 2004). However, an infinite range of alternative methods can be used to prepare genomic representations for DArT.
DArT operates on the principle that the genomic ‘representation’ contains two types of fragments:
- Constant fragments, found in any ‘representation’ prepared from a DNA sample from an individual belonging to a given species, and
- Variable (polymorphic) fragments called molecular markers, only found in some but not all of the ‘representations’.
The variable fragments are informative because they reflect sequence variation that determines the fraction of the original DNA sample that is included in the ‘representation’. We call the variable fragments DArT markers. Their presence vs. absence in a genomic ‘representation’ is assayed by hybridising the ‘representation’ to a DArT array consisting of a library of that species.