Is this what farmers have been waiting for?

Based on promising early results, “epigenetics” may help save agriculture from climate change

In the past 25 years, the agricultural landscape has seen several significant changes, from the advent of herbicide-tolerant crops to precision agriculture systems and soil supplements. Many were dubbed game changers when they were introduced, and we’re glad to have them all, but they also met with unexpected issues like weed resistance, or they didn’t evolve as fast as expected for other reasons.

The science of genetic alterations — RNAi silencing or CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology — has also come with great potential for improving plant breeding and enhanced traits. But it too has its challenges, including regulatory agencies in Canada.

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The field of genomics is still in a state of growth as it searches for the best ways to enhance plant performance and productivity. At the same time, regulatory agencies are still haggling over definitions and applications. When is a genetic manipulation a “plant novel trait” (PNT)? When is the precautionary principle impairing scientific discovery to its detriment?

Epigenetics has been around for decades but it’s only been recently that researchers have started to manipulate it for field crop advantages, including the development of plants capable of withstanding stress such as drought, heat or cold.

Although there are questions surrounding the reaction of Health Canada or the Canadian Food Inspection Agency (CFIA), one U.S. researcher has uncovered a world of potential for this form of genetic manipulation.

Better yields and resilience

Epigenetics is defined as “the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence.” In effect, it changes gene expression without altering the genetic makeup of the plant. These changes occur naturally and often in an organism. In humans, as we know, genes can be silent during childhood, then be “activated” as a person ages, and vice versa.

Another example is that some genes are active in an eye cell, for example, yet are completely silent in a kidney cell. Epigenetics is the vehicle for different tissues taking on specialized functions.

In plants, epigenetics can oversee alterations that shift reactions from normal growing conditions to ones that adapt to more stressful conditions, such as drought or cold tolerance. A control point for influencing these epigenetic traits was recently discovered in the plant gene MSH1, a discovery made by Dr. Sally Mackenzie and her colleagues in 2012. Mackenzie had been studying the role of the mitochondria that are responsible for respiration and energy generation in plant cells, trying to understand their influence on plant fertility and their ability to disrupt pollen development.

“It was only later that we found out that MSH1 operates not just in mitochondria but in a different compartment: the chloroplasts,” says Mackenzie, a professor of biology and plant science at Penn State University. “That compartment has an ability to trigger epigenetic changes, and it was purely serendipitous that we discovered this, and we were off and running in a totally different direction.”

Dr. Sally Mackenzie (right) with PhD candidate Hardik Kundariya (centre) and Dr. Xiaodong Yang (left) at work in the laboratory.
photo: Courtesy Dr. Sally Mackenzie, Penn State University

In effect, her method silences the MSH1 gene in plants growing under normal conditions. Because of this, the plant behaves as though it’s growing under stressful conditions and it activates compensatory mechanisms that allow it to cope with temperature, drought and pathogen stress.

Manipulating these “reprogrammed” plants through crossing or grafting results in higher yields and greater resilience.

In a one-year trial with an elite tomato variety, Mac­kenzie saw a 29 per cent yield boost under ideal conditions. Researchers have also seen striking gains in tomato plant resilience under heat stress conditions in the field.

Mackenzie believes that genetic enhancements under less-than-ideal conditions will result not only in better yield stability, but also enhanced resilience in the plant.

Although the MSH1 gene was originally cloned in 2003 for mitochondrial research, it wasn’t until 2011 that Mackenzie and her lab colleagues made the discovery about its influence on chloroplasts. Since then, she’s successfully applied the MSH1 method to sorghum, tomato and soybeans for enhanced field performance, and has begun greenhouse work in canola and strawberries. She’d also like to test alfalfa for increasing above-ground biomass, as well as grapes, various tree crops, cotton and potatoes, although for that she requires more funding.

The climate threat

There’s an urgency to Mackenzie’s work, as she believes agriculture isn’t adjusting rapidly enough to really address climate change.

“In the next 30 years, it’s clear that crop production strategies will have to adapt, but there isn’t a lot invested in what that process should look like,” Mackenzie says. “I’m hoping that people will reflect on the idea that epigenetics is one tool that we haven’t had in our toolbox that might offer, not a full solution, but at least one potential remedy. I worry that we’re going to keep our strategies the same and we’re going to get caught with larger losses each year when that flood or that drought comes, and we haven’t come up with crops that have a level of resilience to tolerate those changes.”

The right method

The method by which these genetic manipulations can occur allows for two different breeding approaches. The first — and the fastest — is to graft an MSH1-modified line as rootstock to an unmodified line and harvest the seed from that combination. The modification has been introduced already, so imparting a genetic enhancement occurs by the next generation. The second approach is through conventional crossbreeding.

“In crops that can be grafted, which would apply to soybeans, tomatoes and any dicot species as well as grapes and tree crops, it works wonderfully, and that’s the most rapid way to introduce the method,” says Mac­kenzie. “There are lots of crops that offer something valuable to our studies as we find out how much impact this system can have on any individual crop that has the cultivation properties. Potatoes would be great because they’re vegetatively propagated, so once you carry out the manipulation and find the perfect crop features, you can propagate that in perpetuity because they never go through seed.”

If breeders don’t get serious about climate change, the losses in crops like soybeans may be catastrophic, Mackenzie says.
photo: Supplied

Although she’d like to work with wheat and corn, the two crops present different challenges, over and above sufficient funding. The wheat genome is a polyploidy, so it is unclear how effectively the current gene silencing method would work. On the corn side, she concedes there’s reluctance within the sector’s research and breeding efforts to focus on much aside from yield and the current F1 hybrid model. She notes that recent yield improvements in corn have been largely due to increased plant densities.

“To me, that is not a long-term strategy, but as long as the industry is fixated on that, I don’t see them looking for innovations in other areas,” says Mackenzie. “And because they’re so recalcitrant to change, we’ve been slower to move into corn.”

The one constraint to introducing methods designed to stabilize yield in the face of climate instability (instead of just increasing yield) is that the industry is not yet open to novel, out-of-the-ordinary breeding strategies for stability. Newer methods, like MSH1, must conform to the standard breeding protocols within each crop. If the tomato sector uses a hybrid, then the method has to be hybrid-ready; if it’s a plant that breeders don’t want to graft, then Mackenzie has to shift to crossing.

“Often, they will only consider a method that gives them a predetermined yield gain, which doesn’t consider yield stability as equally valuable,” she says. “While this is certainly the decision of an industry partner, it does imply that there is not yet a true sense of urgency regarding climate change.”

Regulatory relief

The good news on epigenetic discovery is in its acceptance from a regulatory standpoint. According to Mac­kenzie, the standard practice when dealing with an agency such as the Animal and Plant Health Inspection Service (USDA-APHIS) is to fill out a submission form, send it in and await a decision. With her epigenetics method, APHIS representatives asked her to address their officers in person.

“The technology we were using was so distinctly different from anything they’d ever evaluated that they needed to make sure they understood what we were doing,” explains Mackenzie. “I was in front of that panel for more than two hours, with question after question.”

The ultimate question was, “What exactly would we regulate?” Mackenzie’s response was, “Precisely.”

Epigenetic changes in plants are constant. The only difference is the way Mackenzie induces it. The modified plant would be indistinguishable from a plant that’s under extreme stress.

“This isn’t something you could regulate even if you wanted to, insofar as there isn’t a genetic change that occurs, and although gene expression is altered, many of the alterations naturally occur in a plant that’s under stress,” Mackenzie says. “How do you say that a plant undergoing these gene expression changes under stress is compositionally different from a plant where we’re creating that stress using this manipulation?”

It’s why the panel concluded there wasn’t anything to regulate, since there hasn’t been a tangible change in the crop to follow. Mackenzie reasons that if that same conversation played itself out in Canada, regulators might come to the same conclusion.

But it will take leadership, says Mackenzie. “Part of the regulatory terrain has been complicated by the fact that various aspects of CRISPR and other cisgenic technologies are just now coming out, and until the dust settles on all of that, we’re kind of in limbo also.”

About the author

CG Production Editor

Ralph Pearce

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