Patrick Masson likes to confuse plants. In his lab, the CALS professor of genetics grows seedlings of the Arabidopsis plant in Petri dishes set at a sharp incline, deliberately jumbling the natural cues plants use to figure out how to grow. The setup causes the plants’ roots to skew down the surface of the plate in tiny waves, as if they didn’t know which way to turn.

From the plants’ confusion, Masson finds clarity. The root growth patterns are helping him study the molecular mechanisms plants use to sense important information about their environment, such as which way is up and the location of rocks or other obtrusions that might hinder root development.

In the process, Masson is contributing to an overlooked field of study that may be poised to revolutionize agriculture. Roots, largely ignored by plant breeders in their attempts to boost crop yields, are gaining attention as a target for new efforts to optimize plants. “Because breeders have not taken full advantage of root architecture as a way to improve yields, there is a huge genetic potential for improved production through breeding,” explains Masson. “Hopefully, these efforts will lead to a new Green Revolution.”

The Green Revolution, a decades-long period of intense crop breeding that began in the 1940s, led to massive yield increases in wheat and rice. But those efforts rarely focused on root systems, which, hidden beneath the soil, proved harder to assess than above-ground traits. Now, scientists have perfected ways of growing plants in clear, nutrient-rich agar gels, making it easy to monitor root growth in the lab. In Masson’s case, he grows Arabidopsis seedlings on dense agar that the seedlings’ roots can’t penetrate, which forces the roots to skew and wave down the agar’s surface as if they had encountered a large rock in the soil.

After nearly two decades of studying root systems, Masson has discovered a number of genes and proteins that affect root growth, including one involved in the transport of an important plant growth regulator. Plant breeders are beginning to target some of these root-forming genes to improve plants’ tolerance to drought or acidic soils, says Masson. In one effort, breeders are developing new varieties of wheat for arid climates by crossing popular cultivars with varieties with extra-long roots that can tap into water deep below the earth’s surface.

The first agricultural application from Masson’s lab, however, will likely benefit the biofuels industry. In his root studies, Masson discovered a gene that helps regulate the amount of lignin that gets deposited in plant cell walls throughout the entire plant—both below and above ground. With funding from the Great Lakes Bioenergy Research Center, he is now further assessing this gene.

“To generate better biofuels,” he says, “breeders would want to decrease the plant’s lignin content” by dialing down the gene’s activity. The best way to do that, it turns out, may be to start at the bottom.