[1][2][3] The general steps involve reducing the complexity of the genomic DNA with specific restriction enzymes, choosing diverse fragments to serve as representations for the parent genomes, amplify via polymerase chain reaction (PCR), inserting fragments into a vector to be placed as probes within a microarray, and then fluorescent targets from a reference sequence will be allowed to hybridize with probes and put through an imaging system.
[1][2][4][5] It also afforded low costs and faster results compared to related solid state DNA arrays that detected Single Nucleotide Polymorphisms (SNPs).
[1][2] Since its inception, the technology has been a major instrument in the analysis of polyploid plants as well as in the construction of physical and genetic maps to understand relations between species based on similarities and allelic variances among their genomes.
[1][2] A byproduct of their discovery of a fast, low-cost whole-genome profiling method was that it also provided with the identification of SNPs as well as base-pair insertions, deletions, and shifts, which is an added layer of allelic variation between species analyzed.
[1] The analysis consisted of detecting the presence, or absence, of specific DNA polymorphisms with probing arrays as well as quantifying the strength of each signal, via fluorescence, within the subspecies.
[2] This step of the process deals with reducing large complex genomic DNA of selected species into more, manageable fragmented components through the use of specific restriction enzymes.
It is eminent to avoid repetitive sequences when selecting fragments as these will exhibit the lowest amount of polymorphism within analyzed genomic DNA.
Following addition of the fluorescent dye, targets are added to microarray probes containing the amplified E. coli clones where denaturing and subsequent hybridization, if possible, takes place.
Following hybridization, slides are washed and scanned with an imaging system that targets fluorescent signals with the incorporation of an open-source software called DArTsoft.
[2][8] In its inception, DArT was used to develop phylogenetic cladograms of rice subspecies based on the presence or absence of DNA fragments in each species’ genome.