British researchers turned off a plant gene this year without modifying its DNA sequence.
There is a shortage of food in many areas of the world, and the situation is expected to decline through extreme weather and climate change. Genetically modified organisms (GMOs) are a possible solution to improve crop resilience, production, and sustainability through harsh climates. There have been many concerns about GMOs, though, particularly through Europe which has resulted in regulatory difficulties globally. The leading agricultural-biotechnology company Monsanto has been a lightening rod for concerns surrounding allergies and the use of foreign genetic material, amongst other things. What if plants could switch their genes on and off, depending on which traits were important in a certain climate, instead of permanently modifying the underlying DNA? This is the allure of epigenetics, or the study of chemical markers sitting over a DNA sequence that regulate genes. Epigenomic modifications do not affect the building blocks of DNA (nucleotides) thus do not permanently change it.
Epigenetics[caption id="" align="alignleft" width="219"] Photo: Wikimedia Commons[/caption]
According to (www.whatisepigenetics.com): “Genetic modifications happen naturally and farmers have been taking advantage of this phenomenon for centuries by cultivating plants with desirable characteristics. This does, however, take some time to perfect. So why not explore a different approach. Could crops be improved without directly editing their DNA? Plant scientists are already working on this and their findings offer tremendous promise for better performing crops without gene mutation. Their research, of course, is in epigenetics.”
“The study of epigenetics deals with heritable changes in trait variations that are not caused by alterations in DNA sequence. DNA methylation, histone modification and RNA interference (RNAi) are three commonly used mechanisms for epigenetic gene regulation in plants. Once these epigenetic changes are established, it’s possible for them to be inherited from one generation to the next. Inheritance occurs through epigenetic alleles (or alleles having the same DNA sequence but different DNA methylation patterns), which in turn leads to higher polymorphism and eventually to newer phenotypes. This new source of variation is vital to the crop improvement process. Plant breeders already know that heritable variation provides basis for selection in plant breeding. Therefore, because novel phenotypes are obtainable through epigenetic processes, there’s great potential for epigenetics to improve crop production.”
Turning Genes Off/On
In March 20113, a team of researchers at the Salk Institute for Biological Studies investigated whether plants could turn their genes on or off via epigentics depending on optimal traits in a certain climate. The series of studies was conducted on Arabidopsis thaliana, a common mustard weed across the Northern Hemisphere (Scientific American: Can Epigenetics Help Crops Adapt to Climate Change?). According to Scientific American (Tiffany Stecker): “Genetic adaptation occurs through evolution — which can take hundreds of years. Adaptation through epigenetics might happen much faster, said Ecker. For the mustard weed A. thaliana, a plant that can reproduce a new generation every eight weeks, Ecker and his colleagues have observed what looked like epigenetic modifications after 30 generations, or about five years.”
The feat was repeated again this year (March 2015) in the UK according to Science In The News @ Harvard (Epigenetics and Plant Breeding: Hard Science, Soft Tool):[caption id="attachment_2105" align="alignright" width="276"] Photo: Wikimedia (Arabidopsis_thaliana_rosette)[/caption]
“As reported in Proceedings of the National Academy of Sciences (PNAS) this year, a team of British researchers were also able to completely shut down a gene in a plant without making any modifications to its DNA sequence. If silencing a gene is found to lead to valuable properties for a crop, then this strategy may produce seeds with improved traits, but no genetic modifications. This means that improved traits are no longer obtained by adding foreign DNA into a plant, but rather simply by inactivating what is already there. In this way, the question of heritability is of importance. Will the seeds bear improved traits for one or two generations and turn back to their natural state without repeated treatment? Or will they conserve their traits indefinitely like classic GMOs? The number of generations the trait is transmitted is thus very important, as it will impact the economic models used by companies and farmers.
Using viruses to inject the small RNAs, Baulcombe and Bond targeted a gene that actively inhibits flowering. If the RNA-mediated silencing worked, the inhibitor would be inactivated and the plants would flower early. The plants infected with the viruses did not flower early, and many of their progeny were also late-flowering. But a small percentage of their offspring did flower early. The second generation was even more affected. As the offspring of intermediate-flowering plants flowered early, it was as if the silencing was progressively increasing between generations. When the plant antiviral defense mechanisms were inactivated in a separate experiment, the researchers turned this small percentage of offspring that flowered early into almost 100%! These early-flowering plants were all free of the virus because only the parents were infected. The inactivation of the inhibitor was found in the pollen of the parents, but not at all in their leaves. This confirmed that although silencing began to occur in the parents, it was too late in development to be seen in the leaves, and it was instead transmitted to the offspring by the pollen after at least two generations. This is the first proof of the feasibility of heritable, epigenetic silencing of naïve genes.[caption id="" align="alignleft" width="317"] Photo: Wikimedia Commons[/caption]
Taking this first proof of concept from the laboratory to application in the field will require a number of questions to be answered. Over how many generations does the silencing last? Can we increase the efficiency without getting rid of the plants’ antiviral mechanisms? And foremost, how can we avoid spraying genetically modified viruses in our fields? If another carrier of the small RNAs could be used, this would be a viable strategy to entirely bypass genetic engineering. Indeed, as Baulcombe and his collaborators did, we can now change a trait of a plant without modifying its DNA. The trait Baulcombe’s team targeted, reduced flowering times, is of agronomic interest and could improve a crop’s adaptation to local environments. Other interesting traits could also be studied; for example, resistance to drought, heat-shock, and flooding. If silencing a gene is found to lead to valuable properties for a crop, then this strategy may produce seeds with improved traits, but no genetic modifications. This means that improved traits are no longer obtained by adding foreign DNA into a plant, but rather simply by inactivating what is already there. In this way, the question of heritability is of importance. Will the seeds bear improved traits for one or two generations and turn back to their natural state without repeated treatment? Or will they conserve their traits indefinitely like classic GMOs? The number of generations the trait is transmitted is thus very important, as it will impact the economic models used by companies and farmers.”
If further research shows that epigenetically modified organisms (EMOs?) conserve their traits indefinitely, it may be a solution for sustainable food production in harsh climates without the allergic concerns of GMOs.