Whitney Palmer

Durham scientists study plants for biofuel production

Published in the Jan. 23, 2012, Raleigh News & Observer and Charlotte Observer

By Whitney L.J. Howell

These days, downtown Durham is better known for its burgeoning cuisine scene and modernized, reclaimed spaces than its long history with cash crops. The storied days of tobacco curing in the city’s brick factories have been replaced with technology research that could, scientists say, bolster the biofuel industry while creating stronger crops.

Inside its redesigned, sustainable lab space near the Durham Performing Arts Center, GrassRoots Biotechnology uses patented research methods to study plant genes.

The goal, said company co-founder Philip Benfey, is to pinpoint ways to strengthen plants considered useful in biofuel production, such as switchgrass.

“With this research, we’re looking toward the future,” said Benfey, a genomics professor with Duke University Institute for Genome & Science Policy. “Over the past five or six years, as the price of oil has risen, there’s been increased interest in the idea of biofuels. There’s an opportunity to use the discoveries we’ve made in the academic lab in the commercial system.”

GrassRoots, launched in 2007, uses its two technology platforms – RootArray and Root Imaging – to dissect plant gene regulation, understand gene function and identify root traits.

Ultimately, the company wants to use its findings to boost crop yield and strength, Benfey said. It’s an objective that is in line with the Biofuels Center of North Carolina, a General Assembly-funded endeavor that supports biofuel production statewide.

But making better energy sources of biofuel plants like switchgrass may not be as simple as tinkering with the plant’s genetic structure. The part of the plant that makes it useful for biofuels is locked away inside harder, woody parts called lignin. N.C. State biological and agricultural engineering associate professor Ratna Sharma-Shivappa said freeing the lignin can be difficult. Often, she said, harsh chemicals must be used to separate the energy-producing carbohydrates from the rest of the plant.

Making plants glow

The main focus of GrassRoots’ scientists is creating a faster-growing, more

extensive root system in switchgrass, a crop identified by the U.S. Department of Agriculture as yielding high energy levels. Using RootArray, a system Benfey developed, scientists track how gene expression changes from one generation of plants to another, weeding out weak genes and passing along the strong ones.

GrassRoots’ long-time partner Monsanto, the global agricultural and farm production firm, is particularly interested in using the RootArray findings to produce heartier plants that can meet the world’s food and fuel needs, Benfey said.

Douglas Eisner, GrassRoots’ co-founder, said scientists put seeds into the individual holes of a multiwell tray. A promoter gene – part of the plant’s DNA responsible for passing down characteristics – is tagged with green fluorescent protein. The plants grow for up to six days in a nutrient-rich gel environment, and if the tagged gene is passed on, it glows green.

Scientists manipulate each gel environment to see how the plants respond. For example, one tray of plants could be exposed to a high-salt environment, or another to low nitrogen levels. The RootArray process is highly efficient, Eisner said, allowing GrassRoots to test and observe 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,” Eisner said. “If we know how plants will respond to the soil and what their uptake of the nutrients and bacteria is, then we will know what to do so they can cope with their environments.”

Tracking gene expression will help GrassRoots identify the genes and genomic markers that correspond to various traits, presenting the opportunity to breed out weaker characteristics and only pass along traits that make plants stronger.

Such changes, he said, will allow the production of biofuel plants in arid land, places with high salt content, and soil with low nitrogen.

Studying the root

It’s also important to study the roots themselves, Benfey said. Through Root Imaging, scientists take 40 images in a 360-degree view of the roots grown in gel. Those images are used to produce three-dimensional root reconstructions that can be compared with other roots from different varieties of the same plant.

“It’s a way for us to see how various types of the same plant differ,” Benfey said. “We can ask questions about why the differences are there – what makes one variety thrive in a low phosphorus environment (when) others fail. This technique could help us even design roots that better withstand drought.”

Switchgrass is a particularly good crop for this type of study, he said, because some roots grow deep into the ground while others stay shallow but spread out extensively.

Currently, however, switchgrass takes a full growing season to produce any yield. Ultimately, Benfey said, he hopes GrassRoots’ research results in a faster-growing, faster-producing switchgrass that can grow in marginal soil conditions, such as North Carolina’s red-clay environments.

Understanding the root system and knowing what a plant looks like underground is beneficial in many ways, he said.

“We have the capacity to make plants stronger. It’s not just for biofuels, and it’s not just for agriculture. This research and its results are applicable to both areas.”

To read the article on the Raleigh News & Observer website: http://www.newsobserver.com/2012/01/23/1798936/making-biofuels-grow-glow.html

To read the article on the Charlotte Observer website: http://www.charlotteobserver.com/2012/01/23/2950470/making-biofuels-grow-glow.html#storylink=misearch

January 23, 2012 - Posted by wjpalmer | Science | biofuel genetic research, Douglas Eisner, Duke University Institute for Genome & Science Policy, genetic research with switchgrass, genetically altering plants to survive in various soil conditions, GrassRoots Biotechnology, green fluorescent protein in plant genetic research, partnership between GrassRoots Biotechnology and Monsanto, Philip Benfey, plant genetic research to grow stronger plants, Ratna Sharma-Shivappa, Root Imaging, RootArray, tagging plant promoter genes to study genetic inheritance