Since the 2000s advances in science and engineering have led to the development of new technologies in food and agricultural production. In the area of crop breeding, these advances have afforded us the opportunity to decode the genetic blueprint of individual crops so that we can understand their response, or lack thereof, to specific stresses such as fungal attack, drought or prolonged cold periods. This is key to generating more resilient varieties against the stresses of climate change and also against the emergence of novel disease strains.
One such example is the interaction of potato and late blight disease. The late blight organism has the ability to infect potato leaves and within approximately three days to destroy leaf tissue at an alarming rate. During that short three-day period, there are no visible symptoms but within the leaf, the cells of the plant and late blight are in a struggle akin to a scene from Game of Thrones.
Fortunately, over the last decade we have been able to fully characterise this interaction between plant and pathogen. Indeed, we now know that the capacity of a potato variety to resist/succumb to late blight infection is dependent on the efficacy of the variety’s resistant (R) proteins to counter the disease-causing proteins (effectors) of the infecting late blight strain.
Using technologies that have now become mainstream, we know the genetic template for multiple R proteins which originate in wild potato species. By transferring these R proteins into commercial potato varieties, we can test their efficacy against multiple strains of late blight. In turn, this provides insight into how durable the action of the R proteins would be in offsetting late blight epidemics.
Cisgenics bring focus
This is work we have completed in Teagasc with our European partners and we have shown how the dependency for fungicides in potato production can be significantly reduced using these R genes. The physical transfer of these R genes into commercial varieties is reliant on the use of novel breeding techniques (called cisgenics), which, within the EU, is deemed a form of genetic modification.
This means developed cisgenic varieties, which can reduce the environmental impact of potato production by over 95%, must be labelled GM. Due to current EU regulations, this leads to a lengthy and expensive route to commercialisation, making it prohibitive for producers.
Cisgenics is a technique that sees the extraction of a piece of DNA (eg R gene) from one species and its transfer into the DNA of a related species. This can be from wild potato to conventional potato, wild wheat to modern wheat varieties or from wild apple species into elite apple cultivars.
While this process can be done by conventional plant breeding in a crop such as potato, it can take from 13 to 30+ years to get a new commercial variety with the wild trait of interest included. Using cisgenics, this process can be achieved in about three years. Cisgenics is merely accelerating the breeding process and speeding up the transfer of DNA between related varieties or species in a more precise way.
Working within the cell
But what if changing the properties of a plant did not require any material (DNA) to be brought in to a plant to improve its performance? What if it was possible to change the activity of existing genes in a plant to enhance their functionality?
For example, we know there are R proteins within the potato cell that have become obsolete as late blight has evolved to use them as a de-facto lighthouse within the potato cell to guide the way for the late blight effectors to bypass the plant’s defence machinery. Is it possible to turn off this light and, if one could, would it revert a defunct R protein into a viable effective R protein? In effect, is it possible to turn the evolutionary clock back?
In 2013, US researchers published a study which described a technique that could, in effect, achieve this. Termed CRISPR (pronounced ‘crisper’), the technique has led to one of the most exciting scientific stories in a generation. While techniques such as cisgenics transfer DNA from one cell to another, CRISPR is analogous to a molecular scissors, which can be guided to snip/edit the code of a specific target piece of DNA within the targeted cell. As a result, there is no transfer of DNA from one species to another. In contrast, all that is being done, is tweaking what is there already to work more efficiently.
There is no known source of strong genetic resistance to ramularia but some believe that effective control could be achieved where multiple small effects could be identified and activated.
So how is this achieved? CRISPR is a complex containing a small strand of DNA and a specific protein (called Cas9), which is the molecular scissors. The cutting protein has a natural ability to cut DNA pretty much anywhere along a DNA strand, once it is guided to the selected spot that needs cutting. That is where the small strand of DNA comes in. These can be made to match perfectly with any sequence of a target gene and, in effect, then function as a sat-nav for the cutting protein.
For example, a defunct R gene called “mlo” exists in many plant species and, when it is cut at a specific location using CRISPR, it has been shown that the resulting edit reverts the plant from being highly susceptible to powdery mildew to being highly resistant. To date, this has been demonstrated in wheat and tomato and was achieved by making a single cut/edit in the pre-exiting mlo gene. While CRISPR editing is inexpensive and relatively simple to complete, the scientific community has sought to develop this process for decades. However, since its discovery a little over six years ago, CRISPR has become popular in many disciplines of science and scientists now apply its potential to address biological challenges.
As with any new technology, approaches to its adoption must be responsible and fully investigated, but gene editing appears to have great potential for crop research.
Gene editing successes
There have already been many biological challenges solved using gene editing. Mildew resistance has been created in wheat and tomatoes by editing a single gene. It has been used by researchers in Pennsylvania State University to prevent harvested mushrooms from going brown.
Editing has been demonstrated in all of the world’s major crop species such as soya beans, wheat, potato, barley, maize, cassava and rice, as well as a multitude of horticultural crops.
For example, it has been used to make tomato plants immune to Tomato Yellow Leaf Curl Virus. Significant advances have also been made against rice blast fungus which can destroy yields and rice feeds over half the globe’s population each day.
In potatoes, a group in the Netherlands has shown that silencing, or turning off, defunct R genes can effectively turn off the lighthouse and prevent late blight from bypassing the potato’s immune system. This made a highly susceptible variety to late blight resistant again.
CRISPR – an important tool
With so many chemical actives being lost or withdrawn from European producers, we will come to depend more on the capability of genetics to deliver tangible solutions. Novel breeding techniques such as gene editing can be key here to deliver new varieties that require less crop protection. There is no shortage of target diseases for Irish farming with diseases such as septoria, rhyncho, late blight, ramularia and net blotch, as well as powdery mildew and ear blight plus the cereal viruses, always needing to be contained.
The science of gene editing continues to move at an astonishing pace and technical challenges that existed six to 12 months ago have been addressed, making the editing process provided by CRISPR even more accurate, flexible and effective across a multitude of species. Such is the pace of progress that it is not unrealistic to predict resistance to a multitude of stresses in engineered varieties within the next few years but their availability within the EU is questionable due to regulatory constraints.
Outside of Europe, many countries such as the US, Japan, Australia, Canada and others agree that gene editing is a more efficient form of a traditional plant breeding technique called mutagenesis. Regulators in those countries view gene editing as being equivalent to mutagenesis and, as such, it is not regulated.
Mutagenesis
Mutagenesis has been around since the 1950s and it is the process of generating genetic variability by subjecting a plant’s DNA to nuclear irradiation. This process is highly non-specific as the DNA within the irradiated plants is randomly changed or broken. The random nature of this activity means that any useful new variability may be accompanied by other undesirable traits which complicate the breeding process (eg you achieve disease resistance but the new variety matures six weeks later).
That said, mutagenesis has been successful and has helped generate thousands of novel crop varieties over the last 60+ years. There is no regulation on these and successful ones can go straight to market. Examples include Golden Promise malting barley, Ruby red grapefruit, popular Japanese Pear varieties and hundreds of different cereal varieties.
However, in the EU gene editing is considered a GM technique and so at present must be regulated. This is in spite of the fact that editing is a more precise form of mutagenesis. In practical terms, mutagenesis v1.0 is a non-regulated process while gene editing (mutagenesis v2.0) is fully regulated.
The future
So where does this leave us? From a research basis, editing can still be (and will be) used by research teams to study and investigate the function of genes of interest. The disappointment lies in the fact that varieties generated through these studies are very unlikely to make it to market within the EU due to the complexity of the regulatory framework that has been put in place.
With crop protection options being eroded by loss of chemistry, we can only hope that the resolve shown by legislators to reduce pesticide usage is matched by a readiness to accept science-based evidence that indicates the potential of technology-based solutions such as gene editing to this challenge.
Since the 2000s advances in science and engineering have led to the development of new technologies in food and agricultural production. In the area of crop breeding, these advances have afforded us the opportunity to decode the genetic blueprint of individual crops so that we can understand their response, or lack thereof, to specific stresses such as fungal attack, drought or prolonged cold periods. This is key to generating more resilient varieties against the stresses of climate change and also against the emergence of novel disease strains.
One such example is the interaction of potato and late blight disease. The late blight organism has the ability to infect potato leaves and within approximately three days to destroy leaf tissue at an alarming rate. During that short three-day period, there are no visible symptoms but within the leaf, the cells of the plant and late blight are in a struggle akin to a scene from Game of Thrones.
Fortunately, over the last decade we have been able to fully characterise this interaction between plant and pathogen. Indeed, we now know that the capacity of a potato variety to resist/succumb to late blight infection is dependent on the efficacy of the variety’s resistant (R) proteins to counter the disease-causing proteins (effectors) of the infecting late blight strain.
Using technologies that have now become mainstream, we know the genetic template for multiple R proteins which originate in wild potato species. By transferring these R proteins into commercial potato varieties, we can test their efficacy against multiple strains of late blight. In turn, this provides insight into how durable the action of the R proteins would be in offsetting late blight epidemics.
Cisgenics bring focus
This is work we have completed in Teagasc with our European partners and we have shown how the dependency for fungicides in potato production can be significantly reduced using these R genes. The physical transfer of these R genes into commercial varieties is reliant on the use of novel breeding techniques (called cisgenics), which, within the EU, is deemed a form of genetic modification.
This means developed cisgenic varieties, which can reduce the environmental impact of potato production by over 95%, must be labelled GM. Due to current EU regulations, this leads to a lengthy and expensive route to commercialisation, making it prohibitive for producers.
Cisgenics is a technique that sees the extraction of a piece of DNA (eg R gene) from one species and its transfer into the DNA of a related species. This can be from wild potato to conventional potato, wild wheat to modern wheat varieties or from wild apple species into elite apple cultivars.
While this process can be done by conventional plant breeding in a crop such as potato, it can take from 13 to 30+ years to get a new commercial variety with the wild trait of interest included. Using cisgenics, this process can be achieved in about three years. Cisgenics is merely accelerating the breeding process and speeding up the transfer of DNA between related varieties or species in a more precise way.
Working within the cell
But what if changing the properties of a plant did not require any material (DNA) to be brought in to a plant to improve its performance? What if it was possible to change the activity of existing genes in a plant to enhance their functionality?
For example, we know there are R proteins within the potato cell that have become obsolete as late blight has evolved to use them as a de-facto lighthouse within the potato cell to guide the way for the late blight effectors to bypass the plant’s defence machinery. Is it possible to turn off this light and, if one could, would it revert a defunct R protein into a viable effective R protein? In effect, is it possible to turn the evolutionary clock back?
In 2013, US researchers published a study which described a technique that could, in effect, achieve this. Termed CRISPR (pronounced ‘crisper’), the technique has led to one of the most exciting scientific stories in a generation. While techniques such as cisgenics transfer DNA from one cell to another, CRISPR is analogous to a molecular scissors, which can be guided to snip/edit the code of a specific target piece of DNA within the targeted cell. As a result, there is no transfer of DNA from one species to another. In contrast, all that is being done, is tweaking what is there already to work more efficiently.
There is no known source of strong genetic resistance to ramularia but some believe that effective control could be achieved where multiple small effects could be identified and activated.
So how is this achieved? CRISPR is a complex containing a small strand of DNA and a specific protein (called Cas9), which is the molecular scissors. The cutting protein has a natural ability to cut DNA pretty much anywhere along a DNA strand, once it is guided to the selected spot that needs cutting. That is where the small strand of DNA comes in. These can be made to match perfectly with any sequence of a target gene and, in effect, then function as a sat-nav for the cutting protein.
For example, a defunct R gene called “mlo” exists in many plant species and, when it is cut at a specific location using CRISPR, it has been shown that the resulting edit reverts the plant from being highly susceptible to powdery mildew to being highly resistant. To date, this has been demonstrated in wheat and tomato and was achieved by making a single cut/edit in the pre-exiting mlo gene. While CRISPR editing is inexpensive and relatively simple to complete, the scientific community has sought to develop this process for decades. However, since its discovery a little over six years ago, CRISPR has become popular in many disciplines of science and scientists now apply its potential to address biological challenges.
As with any new technology, approaches to its adoption must be responsible and fully investigated, but gene editing appears to have great potential for crop research.
Gene editing successes
There have already been many biological challenges solved using gene editing. Mildew resistance has been created in wheat and tomatoes by editing a single gene. It has been used by researchers in Pennsylvania State University to prevent harvested mushrooms from going brown.
Editing has been demonstrated in all of the world’s major crop species such as soya beans, wheat, potato, barley, maize, cassava and rice, as well as a multitude of horticultural crops.
For example, it has been used to make tomato plants immune to Tomato Yellow Leaf Curl Virus. Significant advances have also been made against rice blast fungus which can destroy yields and rice feeds over half the globe’s population each day.
In potatoes, a group in the Netherlands has shown that silencing, or turning off, defunct R genes can effectively turn off the lighthouse and prevent late blight from bypassing the potato’s immune system. This made a highly susceptible variety to late blight resistant again.
CRISPR – an important tool
With so many chemical actives being lost or withdrawn from European producers, we will come to depend more on the capability of genetics to deliver tangible solutions. Novel breeding techniques such as gene editing can be key here to deliver new varieties that require less crop protection. There is no shortage of target diseases for Irish farming with diseases such as septoria, rhyncho, late blight, ramularia and net blotch, as well as powdery mildew and ear blight plus the cereal viruses, always needing to be contained.
The science of gene editing continues to move at an astonishing pace and technical challenges that existed six to 12 months ago have been addressed, making the editing process provided by CRISPR even more accurate, flexible and effective across a multitude of species. Such is the pace of progress that it is not unrealistic to predict resistance to a multitude of stresses in engineered varieties within the next few years but their availability within the EU is questionable due to regulatory constraints.
Outside of Europe, many countries such as the US, Japan, Australia, Canada and others agree that gene editing is a more efficient form of a traditional plant breeding technique called mutagenesis. Regulators in those countries view gene editing as being equivalent to mutagenesis and, as such, it is not regulated.
Mutagenesis
Mutagenesis has been around since the 1950s and it is the process of generating genetic variability by subjecting a plant’s DNA to nuclear irradiation. This process is highly non-specific as the DNA within the irradiated plants is randomly changed or broken. The random nature of this activity means that any useful new variability may be accompanied by other undesirable traits which complicate the breeding process (eg you achieve disease resistance but the new variety matures six weeks later).
That said, mutagenesis has been successful and has helped generate thousands of novel crop varieties over the last 60+ years. There is no regulation on these and successful ones can go straight to market. Examples include Golden Promise malting barley, Ruby red grapefruit, popular Japanese Pear varieties and hundreds of different cereal varieties.
However, in the EU gene editing is considered a GM technique and so at present must be regulated. This is in spite of the fact that editing is a more precise form of mutagenesis. In practical terms, mutagenesis v1.0 is a non-regulated process while gene editing (mutagenesis v2.0) is fully regulated.
The future
So where does this leave us? From a research basis, editing can still be (and will be) used by research teams to study and investigate the function of genes of interest. The disappointment lies in the fact that varieties generated through these studies are very unlikely to make it to market within the EU due to the complexity of the regulatory framework that has been put in place.
With crop protection options being eroded by loss of chemistry, we can only hope that the resolve shown by legislators to reduce pesticide usage is matched by a readiness to accept science-based evidence that indicates the potential of technology-based solutions such as gene editing to this challenge.
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