The first genome-scale model for predicting the functions of genes and gene networks in a grass species has been developed by an international team of researchers that includes a UC Davis rice geneticist.

The new systems-level model of rice gene interactions, called RiceNet, is expected to help speed the development of new crops for the production of advanced biofuels, as well as help boost the production and improve the quality of one of the world’s most important food staples.

“With RiceNet, instead of working on one gene at a time based on data from a single experimental set, we can predict the function of entire networks of genes, as well as entire genetic pathways that regulate a particular biological process,” says Pamela Ronald, a professor of plant pathology and director of the grass genetics program within the U.S. Department of Energy’s Joint BioEnergy Institute.

Ronald is the corresponding author of a paper on the new systems biology approach published this week in the online Early Edition of the Proceedings of the National Academy of Sciences. The paper describes how Ronald and other Joint BioEnergy Institute scientists worked with researchers at the University of Texas in Austin and Yonsei University in Seoul, Korea, to overcome challenges and develop a network that encompasses nearly half of all rice genes. The paper is titled “Genetic dissection of the biotic stress response using a genome-scale gene network for rice.”

Rice is a staple food for half of the world’s population and a research model for monocotyledonous species — one of the two major groups of flowering plants. Rice is especially useful as a model for the perennial grasses, such as Miscanthus and switchgrass, which have emerged as prime feedstock candidates for the production of clean, green and renewable cellulosic biofuels.

For decades, UC Davis has helped overcome agricultural and environmental challenges related to rice production in the United States and around the world. Today, campus researchers are using molecular biology to better understand how to improve the hardiness and yield of this grain, which plays such an important role in global nutrition and food security.

Worldwide importance

Given the worldwide importance of rice, a network-modeling platform that can predict the function of rice genes has been sorely needed. However, the task has been complicated by the high number of rice genes — more than 41,000 genes compared to about 27,000 genes for the common research plant Arabidopsis — among other important factors.

“RiceNet builds upon 24 publicly available data sets from five species as well as an earlier mid-sized network of 100 rice stress response proteins that my group constructed through protein interaction mapping,” Ronald says. “We have conducted experiments that validated RiceNet’s predictive power for genes involved in the rice innate immune response.”

Ronald and her team also showed that RiceNet can accurately predict gene functions in maize, another important monocotyledonous crop species.

A RiceNet website is now available to researchers around the world. At the Joint BioEnergy Insitute, RiceNet will be used to identify genes that have not previously been known to be involved in cell wall synthesis and modification. Researchers are looking for ways to increase the accessibility of fermentable sugars in the cell walls of biofuel feedstock plants.

For more information about Ronald’s research, visit her website at

For more information about the Joint BioEnergy Institute, visit the website at

Co-authoring the PNAS paper with Ronald were Insuk Lee, Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh and Edward Marcotte.

This research was supported in part by the Joint BioEnergy Institute through the Department of Energy Office of Science.