Changes to a single gene in a model organism in plant biology, Arabidopsis thaliana, have been found to promote faster-growing and larger root systems—an application that could help researchers engineer bigger, better crops capable of sequestering more atmospheric carbon. The gene and its operations are described in the November 11 issue of the journal Cell.



Bigger root systems mean more climate-warming carbon could essentially be buried, because plants build their roots using atmospheric carbon. From the roots, carbon can be transferred into soil where it can remain for millennia.



Plants engineered to have bigger root systems could also help address food shortages and aid in efforts to grow crops in a warmer, drier climate. Evidence suggests that plants with larger root systems are more drought-resistant.



There could also be benefits to the biofuel industry. Faster-growing root systems could allow new plants to take hold more quickly, including perennial grasses like switchgrass and Miscanthus, which are considered viable feedstocks for next-generation biofuel.



"With switchgrass, for example, frequently you cannot harvest the first year's crop because it takes a long time for the root system to establish," says study author Philip Benfey, a professor of biology at Duke University and director of Duke’s Institute for Genome Sciences and Policy Center for Systems Biology. If plant genetic engineering could reduce that waiting time, "that would be a huge boon for farmers," he adds.



Tissue growth in plants is a complicated process involving many genetic factors. But when Benfey’s group set out to discern which factors most influenced root development, they had a good idea where to start looking. In Arabidopsis, as in most plants, there is a specific zone near the tip of the root where stem cells transition from a stage of proliferation to one where they differentiate into specific tissue types. In this zone cells change from a state of rapid division into one in which they drastically increase their volume by elongating—the first stage of differentiation. "We knew the location existed, but what we didn't know was how the process was controlled," Benfey says.



Based on previous work, the researchers had reason to think it was controlled by transcription factors—proteins that control the expression of certain genes by binding to DNA at specific locations to induce (or block) the transcription of information from DNA to RNA. Also from previous work, they knew the genes whose expression within the transition zone was higher than elsewhere in the cell (indicating that they were being "turned on" for this specific purpose). "We focused on genes that turned on right at that transition," Benfey says, "and among those genes, we focused on transcription factors."



By studying Arabidopsis plants for which the genes for these transcription factors had been selectively knocked out, the group identified a single transcription factor that when inactive resulted in longer roots. They dubbed the gene that codes for it UPBEAT1 (UPB1). Further study revealed that UPB1 regulates the expression of three genes, called peroxidases, which themselves control the distribution of two chemicals, hydrogen peroxide and superoxide, in the root. The precise balance between the two compounds controls the transition from cell proliferation to differentiation. "It appears that UPB1 is a pretty key regulator of this process," Benfey says.



Benfey notes that these bigger, faster-growing plants are not the result of the insertion of a novel gene, but rather a decrease in UPB1's normal activity. "We're not talking about transgenic plants here," he says. In practice this means they wouldn't be subject to the extensive regulations governing the use of transgenic plants, and would thus be much cheaper to put into the field.



Practical application is still several steps away, however. One of the first orders of business is to see if this finding can be applied to other crops besides Arabidopsis.



Benfey is confident. His company, GrassRoots Biotechnology, has acquired the patent for UPB1 , and plans to use it to further explore root development, with the goal of producing even more advanced biofuel crops. He thinks UPB1 is the first of "probably several" genes that have similar functions. "When we understand them well and can control them, we should be able to regulate root activity," just like modern agriculture has successfully altered activity aboveground, he says.