Agriculture around the world faces a myriad of problems: Pests, weeds, random and extreme weather, and drought, to name a few. While none of these issues are new, because of climate change in particular, several of them are being exacerbated. Techniques like genetic engineering, artificial selection, and mutagenesis have made great strides in producing crops with novel or enhanced genes that can tackle these issues.
But modifying genomes and focusing on the identity of genes can’t be the only solution, a multifaceted approach is needed to handling these issues. One idea that has been investigated by crop scientists is modifying a gene’s behavior through altering a plant’s epigenome. The idea is still in its infancy and faces many challenges, but experts believe epigenetic modified organisms (EPOs) may hold a great deal of promise for offering solutions to these agricultural problems.
Epigenetics describes how cells regulate the amount of product (usually this means a protein) that comes from a gene. Cells regulate this by making physical changes to their DNA without changing the sequence (i.e. the order of A, C, G and T) of the gene. This leads to potentially heritable changes in a gene’s activity—i.e. a gene is turned on-off or production is decreased-increased. While they may seem subtle, epigenetic changes can lead to drastic alterations in the way an organism looks and behaves. For example, epigenetics can explain why identical twins (who have the same genome) can have differences in their appearances.
All organisms from bacteria to humans utilize enzymes to make these epigenetic changes. While they often make epigenetic changes due to internal stimuli (like a hormone or a message from a neighboring cell; a process which is vital to early development), environmental factors (like diet) can influence epigenetics changes too.
In plants, researchers have linked abiotic stresses, like cold weather and drought, with epigenetic changes. In particular, they have focused on methylation levels on DNA in response to these stresses. Methylation is one of the most common epigenetic processes, and happens when a methyl group (a small molecule composed of a carbon and a few hydrogens) is attached to a gene. This normally inactivates the gene and the more methylation on a gene generally means a greater degree of inactivation. Think of it this way: there can be so many methyl groups on a gene or a specific area of the genome, that the enzymes needed to make the protein from the gene just can’t access the gene’s instructions.
Scientists have now found that when crops are exposed to these environmental stresses, methylation levels appear to change in targeted ways and many of these changes are permanent (i.e. heritable to the next generation). Some data suggest that more methylation leaves rice plants in a static state which reduces their ability to adapt to a drought, while rice with less methylation have been found to be able to tolerate droughts better possibly because it leaves the plant in a more “plastic state.” However, it may not be so simple as more methylation is bad and less methylation is good. More likely, researchers will need to determine specific genes to silence or over express to create optimal crops. Some data suggest that even between genetically similar rice species, the genes that should be repressed and activated for drought tolerance may be different.
Epigenetics also holds promise in improving crops outside of the fields of environmental stress. Researchers have found that by using epigenetic changes to silence one gene (MutS HOMOLOG1) which is involved with DNA replication, tomatoes show robust yield increase. Other research has focused on developing crops with enhanced nutrient profiles. In a similar way as golden rice, epigenetic changes could lead to more nutritious crops that are fortified with more vitamins.
Obstacles to EPOs
While emerging robust data show that epigenetics plays an important role in a plant’s phenotype, there is still some debate centered around how permanent the changes made by epigenetic engineering will be. Its also possible if the plant, in the fields, will undo the modifications because epigenetics is a constant process in an organism. Also, we know genetics plays a significant role in a plant’s phenotype, that’s why scientists have been so successful with genetic engineering. But there is still some debate as to how important epigenetics is for many of these traits. While they may influence drought tolerance, this influence may not be as strong as predicted.
Another issue will be regulatory, and what extent the proponents of biotechnology will push back against EPOs. It’s arguable that crops that have had their epigenome altered will be considered by both regulators and activists the same as GMOs. One reason this may be the case is that GMOs and EPOs can use similar creation methods. For example, the genome editing technique CRISPR has been modified so that researchers can make epigenetic alterations changes. While the U.S. government has yet to weigh in on how it will see CRISPR created GMOs, anti-biotechnology activists have made it clear that they want crops edited with CRISPR to be regulated the same as other biotechnologies.
Despite these obstacles, research into epigenetics in agriculture is expanding. University of Minnesota and Penn State were recently awarded $3.4 million and $1.2 million respectively to explore the role of epigenetics in crops by the National Science Foundation. If these and other projects provide more promising results, EPOs could be a vital tool for agriculture.
Nicholas Staropoli is the Associate Director of GLP and Director of the Epigenetics Literacy Project. He has an M.A. in biology from DePaul University and a B.S. in biomedical sciences from Marist College. Follow him on twitter @NickfrmBoston.