Over 5 Years of DArTseq Genotyping in Africa

Here at SEQART, we offer GBS services using DArTSeq Technology, just like our mother company Diversity Arrays Technology Australia.

As it was in the case of DArT method, the core of DArTseq technology, is a genome complexity reduction concept.

Many methods have been developed to reduce genome complexity for genomic characterisation, however the DArT methods provide a significant advantage via an intelligent selection of genome fraction corresponding predominantly to active genes. This selection is achieved through the use of a combination of Restriction Enzymes which separate low copy sequences (most informative for marker discovery and typing) from the repetitive fraction of the genome.

While the initial DArT implementation on the microarray platform involved fluorescent labeling of representations and hybridization to dedicated DArT arrays, the DArTseq method deploys sequencing of the representations on the Next Generation Sequencing (NGS) platforms. The transition to the sequencing platform enabled dramatic (1-2 orders of magnitude) increase in the number of genomic fragments analysed and, as a consequence, a corresponding increase in the number of reported markers. As a consequence of the platform change we created even more scalable and cost-effective technology than the initial DArT method.

When DArT P/L was established in 2001, the cost of sequencing of a megabase of DNA was measured in thousands of dollars, whereas at present, it is measured in cents. A drop in sequencing price by several orders of magnitude enabled us to transit to sequencing based genotyping in 2010 – the DArTseq platform was established. The transition to the sequencing platform enabled dramatic (2 orders of magnitude) increase in the number of genomic fragments analysed.

DArTseq for a new organism or application starts with optimization of complexity reduction method(s). While the choice of restriction enzyme combinations is large, DArT P/L has invested considerable effort in testing various combinations on a significant number of organisms and has developed sets of complexity reduction methods (representations) that are performing quite well compared to other methods.

The optimisation process usually selects one dominant method of complexity reduction for the crop, but in many cases several methods were identified which offer application-specific advantages. The difference between the methods can be both quantitative (different number of unique fragments in the representation) as well as compositional (different sets of fragments captured in the representations).

These differences in representation, size and composition translate to different efficiencies in marker detection rate and quality (call rate and reproducibility) and can be further optimized for performance in different applications.