From lab to land: Crop modifications are fortifying our food supply against climate change

Imagine sitting on a shady porch on a perfect summer day, a glass of ice-cold lemonade in your hand. The citrusy tang dances on your tongue as you take a sip. But this simple pleasure is under threat. Rampant citrus disease, extreme weather and intense air pollution jeopardize the lemon trees that provided your refreshment.

Citrus greening, caused by the bacterium Candidatus Liberibacter, or CLas, spreads via the invasive Asian citrus psyllid insect, whose habitat has expanded to Florida, California and Texas as a result of global warming. Infected trees produce misshapen, bitter fruits and eventually die off. Just one of these pests can decimate an entire grove. The disease appeared in the U.S. only two decades ago and could wipe out fresh citrus within the next 15 years.

Kranthi Mandadi, a professor of plant pathology and microbiology at Texas A&M University, wants to ensure that generations after him can enjoy a glass of fresh-squeezed orange juice with breakfast.

“Here in Texas, and around the world, we love our oranges and grapefruits,” Mandadi said. “But the citrus farmers are facing devastating challenges, such as unpredictable weather and water deficit, and I am surrounded by citrus greening, so I wanted to find a way to solve it.”

KRANTHI MANDADI

Kranthi Mandadi, a professor of plant pathology and microbiology at Texas A&M AgriLife Research, Texas A&M University, harvesting grapefruits from a grove during a field trial of their therapies to combat citrus greening.

Thousands of years ago, this bug likely would have appeared gradually over time, Mandadi said. Climate change accelerated that timeline. So scientists like Mandadi and Hiroshi Maeda, a professor of botany at the University of Wisconsin–Madison, have turned to more rapid solutions: genetically and biochemically modified crops.

“Climate change is happening so fast that classical breeding approaches are not enough to overcome the challenges we are facing,” Maeda said. “It took 10,000 years for us to domesticate the crops, and we do not have that kind of time. We must accelerate the process. Using biotechnology, gene editing and transgenic approaches, combined with breeding technology, is critical.”

The spread of citrus greening isn’t the only climate change–induced phenomenon that threatens the food supply. Farmers and scientists face increasing temperatures, rising greenhouse gas levels and mounting climate instability. To overcome these obstacles, researchers like Rebecca Roston, an associate professor plant sciences and the Raikes chair at the University of Nebraska, are studying how cold-tolerant plants adapt to temperature swings to create new staple crops, such as corn, that are ready for tomorrow’s climate.

Public skepticism and regulatory hurdles

Since the advent of modern genetically modified organisms, or GMOs, in the 1990s, food and crop scientists have faced public backlash and struggled to receive funding. According to a recent study of mentions on social media, 32% expressed negative sentiments toward GMOs.

“Scientists and engineers want to be ready when new crops are needed,” Maeda said. “Of course, we shouldn't push the technology if society isn’t ready, but knowing a drastic change in climate is here, it may be now that we need these solutions.”

Developing a strategy to combat disease in plants is the first step.

The Asian citrus psyllid is the insect vector that spreads citrus greening, which is caused by the bacterium Candidatus Liberibacter spp.

However, like most pharmaceuticals, less than 10% of crop solutions make it out of the lab.

“The biggest challenge to transgenic crop releases is the regulatory process,” Mandadi said.
Getting a biopesticide approved by the Environmental Protection Agency can take one to 12 years and usually costs between $5 million and $10 million. Whereas, approval for a GMO seed typically takes over 13 years and costs up to 40 times more.

“As a scientist, I could just say that GMO or CRISPR citrus is a long-term solution,” Mandadi said, adding that approval is at least 10 years away and costs hundreds of millions of dollars. “Hence, even though, scientifically, we know that transgenic crops can work, we took a different approach of biopesticide that is more acceptable to the consumer to get the product faster to the growers.”

Therefore, Mandadi said he prefers to focus on chemical-based or transiently expressed biopesticides for now.

Combatting citrus greening with BMB

Short-term efforts to mitigate citrus greening, such as training dogs to sniff out diseased trees, screening antimicrobial compounds and analyzing the chemical fingerprint of diseased leaves, focus on limiting spread rather than prevention.

On top of that, CLas is almost impossible to study in the lab.

“(The bacteria) is hard to work with because you can't remove the pathogen from the plant itself,” Mandadi said.
“It's an obligate intracellular pathogen so it’s unculturable, or what we call fastidious. … It can take up to two years to test one antimicrobial.”

Mandadi’s group generated a system to screen chemical and genetic antimicrobials against the bacteria. CLas requires a plant vascular system to grow, so they created biological vessels in the form of hairy roots from CLas-infected citrus plants using Agrobacterium rhizogenes. The team used this system to grow CLas in the lab on demand and test various therapies.

“This system is about four times faster than a traditional test that you would do in a greenhouse or in a field trial,” Mandadi said in a Citrus Industry article. “It is not going to replace those trials, but it will step up the speed of preliminary screening.”

KRANTHI MANDADI

Kranthi Mandadi developed the citrus hairy root system to speed the screening of various antimicrobials against the bacterium that causes citrus greening.

Mandadi then developed a solution that could fight infection altogether. His team screened several antimicrobial peptides, originally isolated from spinach, against CLas infection. When they expressed the spinach defensins into the CLas-hairy roots or transiently in citrus trees using a viral vector, they greatly reduced CLas infection and improved fruit yield.

“One of our biggest challenges is to move the discoveries from the lab to the field as (commercial) products,” Mandadi said.

He and his group couldn’t do it alone, so they joined forces with Southern Garden Citrus and Silvec Biologics. The team can deliver the defensins into the trees using a self-replicating virus vector, via grafting without the need for engineering the citrus tree itself. In orange groves, they’ve seen that this treatment improves yields by up to 40%. Now, Southern Garden Citrus Silvec, and Mandadi are seeking EPA approval for this new biopesticide.

Adapting to changing temperatures

Many people think of higher temperatures and heat waves when they think of climate change, but cool seasons are also affected.

According to the U.S. Climate Program Office, the expanding Arctic polar vortex —a strong band of winds in the stratosphere around the North Pole — is bringing extreme winters to parts of the U.S. Colder temperatures stunt the growth and productivity of essential crops such as sorghum, a close relative of corn found in some cereals and pastas.

To combat food insecurity caused by extreme temperatures, Rebecca Roston, the Nebraska plant sciences professor, and Sunil Kenchanmane Raju, Roston’s collaborator and an assistant professor of plant resilience at the University of California Riverside, use omics to make crops like sorghum resistant to chilling stress.

CRAIG CHANDLER, UNIVERSITY OF NEBRASKA, UNIVERSITY COMMUNICATION

Rebecca Roston, an associate professor and chair of plant sciences at the University of Nebraska, studies plants, such as sorghum seen here, to make them more cold-resistant.

“The reality is that the cold has driven human habitation and agriculture for millennia, and it is a problem that is so big that we don’t see it, because it’s opportunity loss, not direct crop loss,” Roston said. “If we could choose to grow plants year-round, we would have much more gain from the same land.”

To fortify crops so they can survive cold spells, Roston’s team turned to sorghum’s cold-tolerant cousin, foxtail millet.

After exposing sorghum and foxtail millet to cold temperatures, the team used whole genomic and lipidomic sequencing to analyze their responses. They found that both grains’ defenses are governed by the circadian clock. However, foxtail millet’s lipid profile showed a few key alterations.

“Circadian rhythms exist across all walks of biology,” Roston said. “Plants have a strong dial rhythm that happens over 24 hours like other animals. … But they also have an additional layer of really strong metabolic influences in response to stresses.”

After a few hours of cold exposure, foxtail millet upregulated the membrane lipid monogalactosyl-diacylglycerol, or MGDG, and eliminated many of its rigid membrane double bonds. MGDG and other unsaturated fatty acids promote fluidity at low temperatures, which may allow foxtail millet to resist membrane sheering when facing cold stress.

The team identified multiple gene candidates for improving membrane tolerance to cold. In their future experiments, Kenchanmane Raju will modulate cold-responsive genes and lipids in sorghum to take advantage of its natural heat tolerance in regions with colder springs.

Playing with gene and lipid expression is a double-edged sword, according to Kenchanmane Raju.

“It’s always a challenge to think about engineering any plants by utilizing these stress-responsive or stress-tolerant genes,” he said. “There’s always an energy cost. So, if you overexpress a particular gene throughout the plant body, there’s always some negative consequences to its growth or other biological processes.”

SUNIL KENCHANMANE RAJU

Sunil Kenchanmane Raju, an assistant professor of plant resilience, recently opened his own lab at the University of California Riverside and will develop single-cell sequencing technologies in plants.

To propel genetically altered crops to the field, Kenchanmane Raju and Roston will need to fine-tune their approach. Few resources exist for single-cell sequencing in plants, meaning that nonspecifically genetically engineering an entire plant can lead to off-target effects.

“There are many ways to mitigate these effects,” Kenchanmane Raju said. “One of them is to try to find out where and when the plant needs the stress-responsive genes. Once we understand this, we precisely engineer the targeted genes to be expressed in the optimal conditions and cell types.”

Roston said incorporating these alterations could be a game changer for farmers, allowing them to move up their growing season without worrying about the risk of early or late freezes.

“To mitigate the effects of high temperatures during reproductive stages, when the plants are much more susceptible, we must think about changing some of the agronomic practices,” Kenchanmane Raju said. “Farmers can try to plant early (when soil is cooler) so the peak reproductive stage does not coincide with the highest temperatures. … I think our chilling stress–tolerant plants are indirectly helping mitigate the effects of high temperatures late in the season.”

Conquering greenhouse gases

Perhaps the best-known consequence of climate change is the disappearing ozone, caused by accumulating greenhouse gases and smog, about a third of which are linked to food production and agriculture. According to Joseph Jez, a Howard Hughes Medical Institute professor of biology at Washington University in St. Louis, a 1% decrease in the ozone layer leads to a 1% drop in soybean yield. Since 1979, the ozone threshold has plummeted by more than 47%.

SEAN GRACIA, WASHINGTON UNIVERSITY IN ST. LOUIS ARTS & SCIENCES

Joseph Jez, a professor of biology at Washington University in St. Louis, and Ashley Sherp, a former Ph.D. student in the Jez lab, work together on understanding metabolic regulatory networks and environmental responses in plants.

“One percent may not seem like much,” Jez said. “But each percent leads to a few billion dollars lost each year by farmers in the American Midwest.”

This decline in atmospheric air quality can exacerbate respiratory and cardiovascular conditions and put pressure on global health systems. With the global population rising, society needs food solutions that don’t exacerbate the greenhouse gas problem.

Hiroshi Maeda, the UW–Madison botany professor, has dedicated his research career to unlocking the mysteries of plant metabolism and developing innovative solutions to combat climate change.

“I’ve always been fascinated with how plants regulate different metabolic processes and control the competition of their growth and chemical production,” Maeda said. “At the beginning of my career, I thought there would be big potential impacts for society in this area, but plant biotech was lagging behind.”

When Maeda and Jez serendipitously found a mutation in the model plant Arabidopsis that increased CO2 fixation by up to 30%, they immediately capitalized on it.

“Nature is always mixing and matching solutions to different molecular, cellular, developmental and environmental problems,” Jez said. “If we understand how plants respond to environmental changes, stresses or challenges, can we engineer them or use pathways from other plants or microbes to give them an advantage?”

Jez and Maeda found that a mutation in the gene suppressor of tyra2, or sota, eliminated a negative feedback loop in the shikimate pathway, a key gateway in aromatic amino acid synthesis in plants. This mutation decouples the plant’s internal regulation, allowing the cells to pump more CO2 molecules into the synthesis pathway. From a structural perspective, Jez said the gene acts like a dimmer switch.

This mutation boosts the capturing of carbon dioxide from the atmosphere. On top of that, the mutant pathway could be utilized to make valuable aromatic compounds, such as woods, pigments, beneficial nutrients, medicine, and even industrial bio-based materials.

“I think our technology provides a very exciting dual benefit,” Maeda said.

SARAH FRIEDRICH, UNIVERSITY OF WISCONSIN–MADISON

Hiroshi Maeda is a professor of botany at the University of Wisconsin–Madison, who studies the evolution of complex plant metabolic pathways across different species to mitigate the effects of climate change.

Now, Maeda and Jez are tweaking this pathway in crops such as soybeans and corn. However, Jez said this is a difficult task because, even though all plants use the amino acid synthesis pathway, each plant species evolved its own regulatory checks and balances.

“When you learn about the amino acid (synthesis) pathway in class, you think, ‘Oh, that’s already known. This is boring; it’s old fashioned,’” Jez said. “But then you realize nature has evolved all of these other little alternative routes and minutiae to do what it needs to do.”

Researchers like Jez, Maeda, Kenchanmane Raju, Roston and Mandadi are racing against time to create cold-resistant crops, novel biopesticides and alternative farming methods to combat climate change’s assault on citrus, sorghum and other crops.

“The plants we have now are not going to be the plants we have in 2050,” Jez said. “The big unknown is whether we can either breed or edit the path forward to make plants survive the climate of 2050 or 2100. Can we do it fast enough while also trying to figure out how to do it with less water and less soil? There are a lot of big systems biology challenges here, but I think that’s where biochemistry, genetics and developmental biology can make a difference.”

These innovations could help ensure enough crops to meet demand — But is society ready to accept GMO foods?

“One way to change consumer sentiments is by gaining their trust. We can each reach out to our friends and family and connect with them to share the benefits of the new technologies and encourage them to share the same with their friends,” Mandadi said. “It’s in our hands to improve foods and save our changing world.”