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Precision Tree Breeding Platform


Our aim is to make DNA marker technologies accessible to the South African forestry industry, including small-scale farmers and production nurseries, other local tree crop industries and academic researchers

Scroll down to learn more about our research service offering

High-throughput DNA Extraction Facility

If you would like to make use of our research service, click on the link below:

In 2021 we established our High-throughput DNA Extraction Facility, which was generously funded by the Department of Science and Innovation and the Technology Innovation Agency. This facility features a GenoGrinder® tissue homogenizer which can grind 576 samples into a fine powder in two minutes, and an oKtopure    DNA Extraction Robot which can process up to 768 samples in a morning. We have several highly trained technicians running the instruments and have successfully applied our protocols to isolate DNA from various plant tissues including leaves, cambium, seed and pollen. A key benefit of the oKtopure    DNA Extraction Robot is the option to decontaminate and reuse selected plasticware, significantly reducing wastage and providing a cost effective alternative to manual DNA isolations.

Since opening this facility we have processed approximately 12 000 samples per year with the capacity to process even more. In 2023, we opened this facility to other users within the University of Pretoria and optimized our protocols to isolate DNA from a range of other tissue types including indigenous plant species, insects and fruit. 



DNA Marker Applications
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Identity verification

We use microsatellite markers for routine analyses such as identity verification of clones, cultivars and varieties. This can be applied to reduce the effects of human error throughout the propagation process, to confirm identity at the point of purchase when buying planting material from a nursery, or to maintain identity in a clonal or cultivar testing trial.


Pedigree analysis

We use microsatellite markers for parentage analysis. This can be applied in breeding programs for applications such as reconstructing pedigrees in an open pollinated trial, confirming the parents in controlled pollination trials, or for backwards selection of optimal parental combinations based on progeny performance.

Pedigree analysis can also be used to infer hybrid status when the species of each hybrid parent is known.

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Species verification

For selected eucalypt and pine species for which genetic profiles have already been developed, we have the ability to verify pure species individuals and to confirm hybrid status. This tool can be used for various applications such as to select hybrid seedlings to plant at a specific site, to identify natural hybrids from a pure species trial, or to confirm the purity of parental species prior to making crosses.

SNP Genotyping

We prepare DNA to and ship it to our international service providers for single nucleotide polymorphism (SNP) genotyping using multispecies Axiom arrays. SNP genotyping can be used to answer more complex questions such as the species composition of individual trees, ancestry mapping in hybrids to determine the species composition at a sub-chromosomal level, and for molecular breeding applications. The latter is performed in collaboration with our industry partners and forms part of special projects designed around their breeding populations.

We have access to two Axiom SNP Genotyping Arrays:

Axiom™ Eucalyptus Genotyping Array (Axiom Euc72K)

This multispecies SNP genotyping array was designed as part of the Eucalyptus SNP Array Initiative (ESAI) and is comprised of 72 000 SNP markers. This number is made up of SNPs that were designed to work across various Eucalyptus species, as well as approximately 4 000 SNP markers specific to the sister genus, Corymbia, and chloroplast SNPs. 

Reference: Grattapaglia D. and Silva-Junior O.B., unpublished.

Axiom™ Tropical Pine Genotyping Array (Axiom Pitro50K)

This multispecies SNP genotyping array was designed as part of the International Pine SNP Chip Consortium. It comprises 50 000 SNP markers which were designed to work across various tropical pine species.

Click here to view the publication

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