Targeted genotyping

We offer cost-effective targeted genotyping technology that empowers breeding and research programmes through affordable genetic analysis.

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Targeted genotyping services

Overview

Our sequencing technologies DArTseq and DArTseqLD have been used successfully to genetically map hundreds of organisms. These methods are effective in reporting randomly distributed markers.

On many occasions, however, there are applications that require genotyping using only a selected marker set. This is targeted genotyping and we have developed three technologies to achieve these results.

Depending which technology we use there is a variance in their marker density capacity and cost. We will always select the technology for each project based on which is most appropriate and cost effective for each client’s needs. We can offer a cost effective solution to practically any application that needs as few as a dozen and up to around 10,000 markers.

Each Targeted Genotype is developed for the specific material and marker sets required by you. For that reason, this service cannot be ordered through our online ordering system. Please contact us if you want to discuss your needs for specific marker characterisation.

Our Targeted Genotyping uses one of three applications developed by DArT – DArTcap, DArTag and DArTmp.

Targeted Genotyping Workflow

Targeted Genotyping Marker Design

DArTag and DArTmp technologies allow for the genotyping of known SNP and small indel markers, with panel sizes ranging from tens to thousands of markers. During the marker design phase, the markers which are to be converted for the targeted genotyping panel will be processed through our proprietary marker design and QC pipeline.

The only essential information required for this is the marker variant information, plus some flanking sequence. The availability of a reference genome assembly is not essential, although the use of a reference assembly can assist in the marker QC and selection process.

A targeted genotyping panel can be designed from your choice of markers.

Additionally, we can convert markers derived from DArTseq and DArTreseq data, providing a very cost effective method for marker discovery in your samples.

A successful targeted genotyping marker panel will match the markers to the material to be genotyped. The DArTag and DArTmp design process gives the flexibility needed to ensure the right combination of markers to avoid ascertainment bias.

The composition of DArTag and DArTmp panels can be updated over time to suit the changing requirements of a genotyping program.

The marker design submission format is described in the document titled Guide For Marker Submission and Specification Form. This document contains the formatting requirements and an explanation of the essential and optional fields in the submission table. This document also provides a form in which to provide instructions on how you would like the marker design and QC to be performed.

An example submission table with descriptive information is available in the document titled Format Instructions For Marker Submission With Examples.

A blank template submission table is also available in the document Template File For Marker Submission.

Targeted Genotyping Pipeline

Important information

When ordering Targeted Genotyping (using DArTag or DArTmp) please note:

DArTmp and DArTag services are processed in 384-well PCR plates, thus we require the services to be ordered in multiples of four 94-well PCR plates. Wells G12 and H12 must be empty for our internal controls.
We can process partial 384 well plates, however the cost per sample will be higher.
Both services require the submission of a positive control (PC)
Minimum 500µl of ~25ng/µl of good quality gDNA in EB buffer (10mM Tris-Cl, pH8.5) shipped in a microtube.
We recommend checking for presence of residual nucleases in your DNA prep as it may degrade the gDNA during transportation. Follow instructions in the FAQ “How can I check DNA quality for DArT assays?”
PC can be shipped as precipitated in Ethanol or as dry pellet. Please indicate DNA storage method and gDNA quantity.
Alternatively, we can extract gDNA for PC in our facilities. Submit enough tissue to obtain 10-12µg of gDNA
Please include a printed copy of the Positive Control Specification document (download below) and all other required documentation. See our ordering pages for the documentation required for sending tissue or DNA, and from inside or outside Australia.

Downloads

To download the following files, visit our Help Centre.

If you require any additional information about the submission of a Positive Control, please contact us.