Building better plants

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By Allyson Mann
Photography by Terry Allen and Jason Thrasher

Lisa Donovan was interested in factors related to climate change long before it become a household term. As a child, she spent summers with her grandparents at Broadkill Beach, Delaware, in a house she describes as a “sardine can stuck on pilings.”

“It was a phenomenal place for a kid to grow up,” she said, with the Delaware Bay and the Atlantic Ocean on one side, and salt marsh—part of the Prime Hook National Wildlife Refuge—on the other. It made her curious about what grew where, and why.

During college she worked in a greenhouse, and as a master’s student, she researched salinity issues in salt marsh grasses. While earning her Ph.D. at the University of Utah, she studied spiny desert shrubs and fell in love with the desert “heart and soul.” Much of her early work focused on the efficiency of water use in desert plants.

Now, 25 years after earning her doctorate, Donovan feels like she’s come full circle. Issues once driven by her curiosity have come into sharp focus under the lens of climate change.

University of Georgia Distinguished Research Professor Lisa Donovan

There’s usually a trade-off between performance and resilience, according to Distinguished Research Professor Lisa Donovan. Plants that grow the fastest or produce the most seeds often are more vulnerable to unfavorable conditions.

“Most of my background comes from seeing a pattern in nature and wanting to explain it,” said Donovan, Distinguished Research Professor and head of the department of plant biology. “Why does this population grow on this slope and something a little different on another slope?”

Such questions are becoming more urgent. The United Nations has estimated that by 2050, the world population will reach more than 9 billion, requiring increased food production. Scientists are debating how much of an increase will be needed, with estimates ranging from 25 to 100 percent more.

But a changing climate makes that more complicated, so researchers are exploring factors like salt tolerance and drought—issues that have intrigued Donovan for years—to figure out the best ways to grow plants in an uncertain landscape.

“Folks are paying more attention now that we realize shifting climate is going to massively affect native plants and agricultural systems,” she said.

It’s not easy being green

In a changing climate, stress tolerance becomes really important, according to Chung-Jui “C.J.” Tsai, Georgia Research Alliance Eminent Scholar and professor of forestry and natural resources, and genetics. She uses model systems to find mechanisms that are applicable to any plants.

“How do you grow crops—whether they are woody or perennial—under changing climate?” she said. “You could improve the wood quality, but it won’t matter if plants can’t grow under limited water and nutrient reserves. The number one priority is harvestable biomass, which means stress tolerance.”

Tsai’s research has shown that overproducing salicylic acid allows a plant to better tolerate drought and heat. However, it negatively affects growth in annual crops.

“We’re testing molecular remedies in the lab to overcome this growth penalty, with promising results,” she said.

A delicate balance

Often it’s about balance—finding a way to bring in one trait without sacrificing or compromising another.

Katrien Devos studies grass genomes including wheat, millets and switchgrass, a forage and biofuel crop. Upland switchgrass, common to drier, colder areas of North America, yields less but is cold tolerant. Lowland switchgrass, common to wetter, warmer areas like the Southeast, yields more but suffers in cold weather, she said. One of her projects involves isolating the trait for cold tolerance and bringing it into lowland switchgrass, creating a high-yield plant that could be grown in more habitats.

University of Georgia researcher Katrien Devos

Professor Katrien Devos is one of many UGA plant scientists searching for ways to help plants thrive in changing conditions. Devos researches a variety of plants including switchgrass (above) and millets. Pearl millet and finger millet are known as orphan crops because they get less attention than crops like wheat and rice, but they’re an important food source in the developing world. Photo: Terry Allen

She also studies seashore paspalum, a highly salt-tolerant turfgrass. It’s a sustainable choice for sports fields and golf courses, and its genetic basis has implications for food crops—if researchers can increase the salt tolerance of cereal crops, then land previously considered unsuitable based on salinity can be used for food production.

“This would particularly benefit the developing world, where land is badly degraded,” said Devos, professor of plant biology and crop and soil sciences. “But interest in climate-resilient crops will increase as climate patterns change.”

Her work also involves orphan food crops, such as pearl millet and finger millet, that are key to food security in semi-arid regions of Africa and South Asia. Unlike the major cereal crops, little research has been done on millets; they lack the molecular tools that have accelerated maize improvement, for example, over the past two decades. Identifying the whole genome sequence—the complete genetic information—for these species offers considerable potential for improvement.

“By working on crops that have undergone little improvement but already are well adapted to adverse conditions, we should be able to make significant yield gains over a relatively short period,” she said.

And progress already has been made—Devos is part of a global team that sequenced the pearl millet genome. The research, published this year in the journal Nature Biotechnology, identified new genetic tools like molecular markers related to drought and heat tolerance.

Good genes

Earlier this year, John Burke and an international team that included Donovan published the first sunflower genome sequence, a project that took about 10 years and, like the pearl millet genome, has implications for climate change.

“As the need for more agricultural products increases, as the population grows, we’re going to have to produce plants that can do more with less,” Burke said.

Key traits related to stress tolerance—the ability to thrive despite drought, salinity and low nutrients, for example—are becoming more important, and the genome is a genetic road map that will help pinpoint the underlying mechanisms that allow a plant to do well in a specific environment. The researchers have markers across the genome that act as signposts, according to Burke, professor of plant biology.

University of Georgia researcher John Burke (left) and Ph.D. candidate Rishi Masalia

Professor John Burke (left) and Ph.D. candidate Rishi Masalia discuss a method for RNA sequencing. Among plant scientists, there is growing interest in exploring what happens below ground, where a plant interacts with the soil, Burke said. Photo: Jason Thrasher

“We can compare different plant lines, establishing correlations between changes in a certain part of the genome and how they respond to the environment,” he said. “It will help us identify, on a genetic level, why one line performs better than another.”

The genome project focused on cultivated sunflowers, which are used primarily for oil. Burke and Donovan are also looking at wild sunflower populations—some of which already have the ability to thrive in compromised habitats.

“A lot of these habitats represent the types of challenges that limit modern agriculture,” Burke said. “They grow in nutrient poor environments, or in a highly saline environment, and they’ve adapted to deal with it. Are there natural variations that we can move into the cultivated crop gene pool to deal with some of these challenges?”

Big data bottleneck

Burke and Donovan have a five-acre field site in California that’s full of sunflowers. It would take half a day just to walk the site, Donovan said, without recording any data.

“The real bottleneck is no longer the lab tools for looking at the genetics,” Burke said. “It’s possible to sequence a genome and genetically characterize a bunch of different lines, but growing the plants and evaluating them is very labor intensive.”

Advances in equipment and technology—the use of tractors, ATVs and drones to quickly collect troves of data, for example—have improved phenotyping, or gathering data on a plant’s physical characteristics (see story on page 32). But linking those massive amounts of information back to individual plant lines requires data processing solutions.

And once that barrier has been surmounted, there’s another. Translating genetic data into a plant with specific desired characteristics is the next big leap, according to Donovan.

“There are 288 different lines in the sunflower project, and we can describe them really well,” she said. “We know lots about the genes, but knowing how we get from there to the plant with the right growth and resilience is more of a black box than we would like.”

Creating cultivars

Research from scientists like Burke and Donovan is speeding up a traditionally slow process and offering new tools for plant breeders. Zenglu Li works in both genetics and breeding for soybeans, using genome-guided research to create new plant cultivars.

Its high protein and oil content make soybeans a globally important crop, with uses including food, animal feed, oil for cooking, biodiesel and ink. Li is working to develop cultivars that are high quality, high yield, resistant to diseases and insects, and tolerant of herbicides and drought.

To help with weed control, he has licensed technology from industry, adding a transgene—a gene taken from another organism—that he hopes will lead to herbicide tolerance. Drought is also a major issue in soybean production, especially in the South.

University of Georgia Soybeans

Associate Professor Zenglu Li (photo at top of story) worked in the agricultural industry before joining UGA, where he continues his research focused on improving soybeans (above). Photo: Terry Allen

“Drought tolerance is a major challenge,” said Li, associate professor in crop and soil sciences. “How can we use less water to get a good yield?”

Like his colleagues across the university, Li is trying to identify a particular gene and relate it back to plants in the field, a time-consuming endeavor.

“Plant breeding is a long process,” he said. “Cultivar development takes eight to 10 years, so development and utilization of new technologies to accelerate the breeding cycle is important.”

The fellowship of the plant

As Donovan tells her students, there’s no one ring to rule them all.  What she means is that there’s no one trait that accounts for plant performance in the field.

“It’s like human physiology. There’s no one marker for good health,” she said. “Everything has to be coordinated and balanced.”

As an ecophysiologist, Donovan investigates how plant processes are carried out in the surrounding environment. Her work is done in the field, the greenhouse and the lab—unlike Burke, who’s mostly in the lab. Though they are co-PIs on a grant, the differences in their backgrounds can be challenging.

“We don’t talk the same language in terms of our training and what we do on a day-to-day basis,” she said. “We practically have to have a cheat sheet of ‘What does that mean?’”

Sometimes their expectations have to be tempered, according to Donovan. For example, Burke will ask her for a trait that makes a plant water-stress tolerant.

“We’ve been studying this for 100 years, and there’s no one trait,” she’ll tell him. “It’s a whole bunch of traits, and it’s context dependent.”

Or Donovan will ask Burke about the genetic basis of a particular trait and get this response: “Are you kidding? It’s not that simple.”

But she believes that both sides are needed to design more resilient crops. Such integration is fostered through UGA’s Plant Center, which cultivates interaction among plant science researchers across the university’s departments, colleges and campuses.

“The best science right now is collaborative,” Donovan said. “That’s actually a fun part. You never get bored in this field.”