Up By the Roots

Jonathan Lynch's lab is addressing global famine with a combination of old-school methods and modern innovation.

This June, agricultural researcher Magalhaes Miguel will make available five new bean types, all of them bred with phosphorus-hunting roots that have the potential to double yields without fertilizer. The scientist is particularly interested in sharing the new lines with farmers and seed companies in places that are in desperate need of better agricultural production--Malawi, Zambia, and his native Mozambique, among them. "I'm excited to see it go out," says Miguel, "because I think our work will have great impact."

The new bean lines come after years of research at the Agricultural Research Institute of Mozambique, where Miguel, who earned a Ph.D. degree in plant science at Penn State in 2012, now works. The methodology is decidedly old school: Every year, Miguel and his colleagues go through each row of their sprouting bean plants, pulling several specimens for what's known as selective breeding--a process led by fellow Penn State alum Celestina Jochua. The better performers have root angles of less than 45 degrees from the stalk, keeping the roots closer to the surface, where the beneficial phosphorus tends to settle.

Getting optimal levels of phosphorus uptake is advantageous for any farmer, but it is an especially useful trait in Mozambique. "One of the main limitations here is low soil fertility," says Miguel. In the United States, he says, this is a problem easily answered with readily available fertilizer. "The problem here is that the farmers cannot afford that," he says. A bag of fertilizer costs about $50 in Mozambique, he adds. More than half of the country lives below the poverty line; most local farmers live on about $1 a day.

Building more efficient plants by breeding for root traits is a method that Miguel and Jochua were introduced to while training under Penn State Professor of Plant Nutrition Jonathan Lynch. For years, Lynch has been leading a global hunt for better root traits: Miguel and Jochua are among dozens of young scientists who have trained under Lynch, part of a growing mass of acolytes to his root-focused research. Lynch's lab also collaborates with research sites around the world, ranging from Arizona to China, intended to span a wide range of climates.

It's a global effort, Lynch says, that is meant to address a global problem: The UN reported in March that 20 million people in Africa face the prospect of famine in the near term. With a world population projected to reach almost 10 billion by 2050 and climate change already having deleterious effects on global agriculture, there is a dire need for practical solutions. "We have 800 million hungry people on Earth," says Lynch. "This is the urgency that compels us every day--trying to help these people."

Old and New

Jonathan Lynch, Manuel Amane, and Magalhaes Miguel evaluate new bean varieties in a low-phosphorus research field at Sussundenga, Mozambique
Jonathan Lynch, Manuel Amane, and Magalhaes Miguel evaluate new bean varieties in a low-phosphorus research field at Sussundenga, Mozambique.

Fighting famine is what first interested Lynch in agriculture. When he was about nine years old, growing up in Northern California, the news was awash with scenes of starvation in Biafra, a Nigerian territory where three million died in the wake of an independence movement and a subsequent Nigerian aid blockade. "I had the notion that somebody had to do something about this," says Lynch. "I resolved to address it."

After earning a bachelor's degree in soils and plant nutrition at UC Berkeley and master's and Ph.D. degrees in plant physiology at UC Davis, Lynch headed to Colombia to work for the International Center for Tropical Agriculture (CIAT). There, he began examining root structures--their architecture, their appearance, their depth, and their dimensions--and breeding for the best traits. "We began a process of finding lines that did much better in low-phosphorus environments, comparing them to lines that did poorly under low- phosphorus environments, and making crosses between these parents," says Lynch, who joined the faculty at Penn State in 1991.

It was a return to a more traditional scientific approach. Researchers had become preoccupied with improving plants at the molecular level, so "old-school" breeding for better traits seemed comparatively quaint--even when Lynch began his work in the late 1980s. "The scientific community had become much more focused on genetic approaches," says Lynch.

Kathleen Brown, a professor of plant stress biology and Lynch's wife and longtime collaborator, stresses that the old-school nature of the roots work and the modernity of biological research don't work in contrast, but in concert. "Technology permits all of this analysis, but it doesn't tell you what you are after," she says. In other words, it's really important to determine the genetic code behind a trait, but you first need to know what traits are really useful. "This work provides the connection."

Plant biologist Kathleen Brown and graduate student Molly Hanlon examine a plate of seedlings in the Roots Lab. Planting a combination of crop varieties that thrive under different conditions could shield farmers in poor areas from total disaster.
Plant biologist Kathleen Brown and graduate student Molly Hanlon examine a plate of seedlings in the Roots Lab. Planting a combination of crop varieties that thrive under different conditions could shield farmers in poor areas from total disaster.

Which is not to say that the couple's lab, informally known as "The Roots Lab," is tech averse--far from it. Field plots are fitted with sensors that measure soil content, and winters are spent analyzing that and data from global research sites, where lines are developed in disparate conditions. "There is a lot of computational work," says Molly Hanlon, who will soon begin her postdoc work at the lab after finishing up her Ph.D. "There is a lot of data that we share with collaborators all over the world." To make the root analysis a bit more efficient, the team works with colleagues at the University of Georgia to develop digital imaging software that can more quickly identify root images. Laser-ablation technology has replaced their razor-blade sectioning; software is employed to simulate natural selection.

The lab also recently received a $7 million grant from the Department of Energy to develop a suite of technologies to facilitate the breeding of deeper-rooted crops, including lasers; ray guns; and Root Robot, a tractor-pulled platform that "excavates, cleans, slices, and images roots on the fly," says Lynch.

One aim of the grant is to spur the discovery of crops that not only offer higher yields but also develop deeper root systems that can better access phosphorus, nitrogen, and water, and capture carbon from the atmosphere and sequester it deep in the soil. With the effects of climate change already impacting global agriculture, says Lynch, more drought-resilient plants are necessary. "The primary limitation of crop productivity on Earth is drought," he says. "That's going to get much worse in the future, according to the climate models."

Lasting Impact

While creating more effective and efficient plants is an aim of the Roots Lab, Brown says training researchers like Miguel and Jochua is similarly essential. "One of the long-term impacts of our lab is all of the people who go on to push the work forward," she says, noting that alumni of the lab often cross-breed the lines developed in the lab with plants that have other desirable traits, like disease resistance.

In addition, the lab's work with maize has attracted the attention of companies in the United States, but--because they're commercial businesses in a competitive environment--they operate in secrecy, so Lynch can only assume his team has contributed to their breeding programs.

But improving corn yields in the relatively wealthy United States is not the lab's main goal, says Lynch. "The big concern is Africa, and the poor countries of Asia and Latin America, where the progress they're making is just not sufficient to keep up with population growth and environmental degradation," he says. "The yields are minuscule, they're 5 or 10 percent of what they should be getting--and that's the primary constraint to food security and economic development," he says. "It's getting worse in many situations."

Better crops, says Lynch, can lead to less poverty, more security, and increased stability. So, will we make it? Will agriculture be able to meet the needs of the Earth's 9.7 billion people in 2050? Lynch says that framing doesn't provide the proper urgency. "For the 800 million people that are hungry today, they feel like their time has run out," he says. "For the three million children dying of hunger every year, they didn't have enough time."

We have 800 million hungry people on Earth. This is the urgency that compels us every day--trying to help these people.

We have the resources and the tools to stop this, Lynch says, and his lab will continue to develop more. But the political will is lacking. "The investments that are being made are not adequate to the task," says Lynch. Part of it, he realizes, is a lack of familiarity with the struggle. "It's kind of like the story about Ebenezer Scrooge, when he visits these different times and places and it softens his heart and it makes him a better person," he says. "I think if Americans could be transported to see what's happening in some village in Mozambique where the people have no food for months on end, they would have a different idea about food security and climate change."

-- Dan Morrell