Green shoots are a sign of spring, but growing those shoots and roots is a complicated process. Now researchers at UC Davis and the University of Massachusetts Amherst have for the first time described part of the network of genetic controls that allows a plant to grow.

Plant stems and roots are built around xylem, long, hollow cells that act both as plumbing — carrying water and minerals around the plant — and as structural material. The structural strength of xylem comes from a secondary cell wall, inside the outer cell wall, which is made either of helical fibers or of perforated sheets. This secondary cell wall is made from three molecules: cellulose and hemicellulose, which are essentially sugars, and lignin, which provides strength.

Researchers interested in making biofuels from plants would like to get the sugars out of plant material without interference from too much lignin.

UC Davis graduate student Mallorie Taylor-Teeples and postdoctoral researcher Miguel de Lucas, working with Siobhan Brady, assistant professor of plant biology at UC Davis, Sam Hazen at U. Mass Amherst and others, cloned 50 genes involved in producing cellulose, hemicellulose and lignin in the lab plant Arabidopsis and screened them for interactions with more than 460 transcription factors, or genes that turn other genes on or off.

With help from UC Davis computer scientist Ilias Tagkopoulos and colleagues at the UC Davis Genome Center, the researchers were able to construct a network showing how the different genes and transcription factors are connected to each other. The results were published online Dec. 24 by the journal Nature.

“This is the first time that such a network has been worked out at this level in a plant,” Brady said. “It helps us think about how these networks are engineered and controlled.”

Notably, the network contains a large number of “feed-forward loops,” Brady said. In an example of a feed-forward loop, transcription factor X acts on factor Y, which in turn acts on gene Z. But X can also act directly on Z. Such systems are well-known in other control networks, reducing random “noise” and allowing precise coordination of different steps without a central core regulator.

The researchers were also able to study how the system reacts to different types of environmental changes. For example depriving root cells of iron promotes lignin production, which increases iron uptake. But exposing cells to salt causes a different response in which xylem cells proliferate to increase water transport.

Understanding the network of controls that influences lignin, cellulose and hemicellulose content might eventually help plant breeders create varieties best suited for harvesting for biofuel production, Brady said.

The findings grew out of more than 7 years work, based on a wide range of data from genetics and plant physiology to computer science and drawing on the resources and expertise of the UC Davis Genome Center as well as U. Mass Amherst, UC Berkeley, the Cold Spring Harbor Laboratory, the U.S. Department of Agriculture laboratory in Ithaca, New York, UC San Diego and the University of Cambridge. Funding was provided by the U.S. Department of Energy, National Institutes of Health, National Science Foundation, USDA, the Royal Society (U.K.), UC Davis and the Hellman Foundation.