DNA Fingerprints - changing the way we look at trees
Ms Melissa Reynolds – DNA Fingerprinting Platform Manager, Forest Molecular Genetics (FMG) Programme
Most people look a little sceptical when I tell them trees have fingerprints too, but they do, only they are hidden in the tree’s DNA. Every tree, if it is not a clonal replicate, has unique patterns of variation within its DNA that distinguish it from every other tree on the planet. Some of its variants affect traits such as tree growth, development and resilience. By harnessing this information, we have the potential to predict the future performance of a tree in the field before it has even left the nursery.
Before we get to all the potential future applications of DNA fingerprinting, let’s rewind. The process of DNA fingerprinting involves taking a short marker sequence of DNA at a known position, where variation is likely to occur and analysing this sequence. This process can be done through one of two techniques, the fully automated single nucleotide polymorphism (SNP) technique or the more labour-intensive microsatellite DNA marker process. For Eucalyptus, we have selected 20 microsatellite DNA markers for routine analysis and the combination of variants at these sites can be combined to give us a unique DNA fingerprint for each tree. We also have a set of 72 000 SNP markers, which are positioned throughout the genome and provide us with a genome-wide DNA fingerprint. The question is, why would we want to know each tree’s unique DNA fingerprint?
There are many applications for DNA fingerprinting, the most obvious would be quality control. Perhaps not as exciting as the more futuristic applications of this technology, but equally important when trying to ensure that the right tree is propagated and ends up at a particular site. In clonal propagation, where you are wanting to make exact replicates of the original tree with the preferential trait, DNA fingerprinting can ensure the correct identity is maintained throughout the process. Bar a few chance mutations, the DNA fingerprint of clonal replicates (ramets) can confirm they are a replica of the initial tree from which clonal material was derived.
In traditional breeding applications where seed and pollen are sourced from different parents, each with their preferential traits, DNA fingerprinting can be used to confirm parentage. We have been using DNA fingerprinting for a while in this fashion and have found that the process not only helps rectify errors like the mislabelling of parental trees in orchards, with individual cases as high as 40% when this technology was first applied, it also identifies areas where new protocols can be introduced to reduce human error.
Quality control will always be an important aspect of what we do. As we use SNP markers to capture more short sequences within the genome, we gain a fuller image of the whole genome, and this opens up new avenues to the technology. Using this deeper understanding of the tree’s genome we can work out how genetic variation affects tree traits like wood properties, pest and disease resistance and tolerance to environmental factors. This is something that has been happening widely in animal breeding and in food crops such as rice. Currently, several projects are underway with Sappi, Mondi and York Timbers aiming to use genomic information to predict the breeding value or future performance of seedlings.
Soon we will be able to take this a step further and use the technology to gain a better understanding of the genetics of site species interactions by looking at how different traits are expressed in different environments. It could even be used to gain a deeper understanding of how specific environmental conditions impact the evolution of genetic traits over time.
With a wealth of possibilities for the technology opening up in front of us, we were confronted with a new kind of challenge – how we process the increasing number of samples beginning to come into the lab. Whereas quality-control trials could see a couple of hundred samples enter the lab process, analysis of genetic diversity at a population level results in thousands of samples. The initial solution was to increase the human capacity in the lab, but in an area of science where it is imperative to minimise human error, fatigue and subjective differences between those doing the sampling, alternative solutions were required. So instead, we opted for robotics. Our lab is now furnished with a robot that can process 768 samples in about two hours. To put this in context, an experienced technician can spend a whole day and only process 192 samples, so it has transformed the efficiency levels in the lab.
With a new robot on the team, industry partners are eager to use the technology to improve the accuracy and efficiency of their forestry operations and a team of scientists at the FMG Programme are ready to apply their knowledge and genomic techniques to a wide array of problems – we are pushing the frontiers of forestry science forward, which is a very exciting place to be.
Meet Ms Melissa Reynolds – DNA Fingerprinting Platform Manager, Forest Molecular Genetics Programme
Melissa never actually intended to have a career working on plants, however, genetics fascinated her as an undergraduate and slowly the allure of studying human genetics gave way to working on trees. Her career in the FMG Programme began in 2008 after her BSc Hons study, when she decided to take a little break from her studies and see where her interests led her. As she had almost no laboratory experience, she started right at the beginning of the FMG DNA fingerprinting pipeline, preparing samples for FMG DNA extractions. Over the course of the next four years, she worked in every position in the DNA Fingerprinting Platform, establishing new protocols and learning every detail of what they do. In 2012, Melissa was promoted to manager of the Platform and has operated in this role ever since, a role in which she managed the DNA fingerprinting of over 70 000 trees that represent much of the elite Eucalyptus and pine breeding material in South Africa. During this time, she was also given the opportunity to complete a part-time MSc degree where she used DNA markers to study genome-wide diversity in the starch tuber crop, cassava. Melissa has always enjoyed puzzles and to her, DNA markers are the puzzle pieces of the genome, and she has endless fun putting these pieces together to answer questions or to tell a story.