Written by Whitney L.J. Howell

Crop scarcity and the demand for greater diversity in biofuels – these aren’t two problems often mentioned simultaneously. But, thanks to Duke University researchers, they’re issues that can be addressed together.

In the mid-2000s, these concerns started to grow, said Philip Benfey, Ph.D., director of the Duke Center for Systems Biology in the Institute for Genome Sciences & Policy. And, based on his work, he knew any answers could lie in plants.

“It struck me that we had the opportunity to address both of these aspects with some of the work we were doing,” Benfey said. “We had an invention and intellectual property, a device called the RootArray that allowed us to grow 60 to 120 seedlings at the same time. It also let us change the environment in which the seeds were growing and look at the responses not of the plant itself, but of the various genes we’d tagged.”

Study results from Benfey’s team led him to launch GrassRoots Biotechnology, a Durham-based start-up company devoted to maximizing crop yield and strength through gene regulation. Their efforts were so successful that agricultural and farm production giant Monsanto acquired the company in 2013.

Using the RootArray technology, the team dissected plant gene regulation, examined gene function, and identified root traits. They chose switchgrass, a high-energy yielding plant, to test the system. Switchgrass is an excellent test plant because its roots grow both deep and shallow, spreading out extensively. Currently, it takes a full growing season to produce any yield, so altering the plant’s genes to survive and flourish in marginal soil conditions could be beneficial for energy production.

RootArray allowed the scientists to track how gene expression changes from one generation of plants to another, weeding out weak genes and passing along the strong ones.

The researchers placed seeds into the individual holes of a multi-well plate. They tagged promoter genes – the part of the plant’s DNA that passes down characteristics – with green fluorescent protein. Plant growth continued for six days in a nutrient-rich gel environment. Any tagged – and beneficial – genes that were passed down glowed green.

It’s at this point where Benfey’s team was truly able to experiment. For example, one plate of plants could be exposed to a high-salt environment while another experiences low nitrogen levels. Overall, RootArray allows researchers to monitor the expression of 100 times more genes than other current technologies.

“Understanding the unique root structure for crops is critical because nutrients are often scarce in soil,” Benfey said. “If we know how plants will respond to the soil and what their uptake of the nutrients and bacteria is this we will know what to do so they can cope with their environments.”

By tracking gene expression, researchers can identify genes and genomic markers that correspond to various traits, making it easier to breed out weaker characteristics and only pass along traits that make plants stronger. Such changes, he said, will allow for the production of biofuel plants in arid land, lands with high salt content, and soil with low nitrogen sources.

Although scientists at Monsanto are now continuing this research into gene expression, having the innovation borne from the knowledge and expertise of Duke researchers gave Benfey an opportunity he said he never anticipated as a faculty member.
“The initial intellectual, patentable invention came out of research conducted at Duke. I’m very grateful to Duke that the initial research upon which the company was built was performed here,” he said. “They let me be a C-suite officer. For that, I am appreciative.”

To read about more Duke entrepreneurs, click here.

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