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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2017-10-09 13:05:23
  • Article ID: 682550

Understanding the Rice Genome for Bioenergy Research

Genome-wide rice studies yield first major, large-scale collection of mutations for grass model crops, vital to boosting biofuel production.

  • Credit: Image courtesy of Guotian Li and Rashmi Jain

    Genome-wide distribution of fast neutron-induced mutations in the Kitaake (a model cultivar) rice mutant population.

The Science

Researchers produced a database of mutations in an important grass crop: rice. To induce mutations they used fast-neutron irradiation. High-energy neutrons induce a wide variety of genetic mutations. Resequencing the 1,504 mutants allowed the researchers to identify structural variants and mutations. The results provide an invaluable resource to improve candidate bioenergy crops, such as switchgrass.

The Impact

Boosting yields of bioenergy feedstock crops such as grasses requires knowing in detail how enzymes and proteins synthesize plant cell walls to modify the processes and the composition. The mutant database offers a functional genomics resource for grass models. These models stand in for the biofuel crop switchgrass. The models are involved in biofuel studies to understand the challenges around plant cell wall synthesis. Until now, mutant collections for grass models have lagged behind those available for the Arabidopsis (flowering plants related to mustard and cabbage) model system.


For more than half of the world’s population, rice is the primary staple crop. As a grass, it is a close relative of the candidate bioenergy feedstock switchgrass. The research team assembled the first major large-scale collection of mutations for grass models. Scientists at the University of California, Davis led the team, which includes researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, and the Joint Bioenergy Institute (JBEI), a DOE Bioenergy Research Center. They used the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), and compared the genes against the reference rice genome of another japonica subspecies called Nipponbare available on the DOE JGI Plant Portal Phytozome.

Through fast-neutron irradiation, the time-consuming procedures involving plant transformation or tissue culture were bypassed, allowing for faster development of rice mutant collections. The DOE JGI resequenced 1,504 rice mutants and identified structural variants and mutations. The work follows a pilot, genome-wide study begun two years ago, in which 41 rice mutants were sequenced and analyzed to identify mutations and structural variants. This new, large-scale collection of more than 90,000 mutations affecting nearly 60 percent of all rice genes is now available on a publicly accessible database called KitBase. The database is a comprehensive resource that will allow researchers to quickly identify rice lines with mutations in specific genes and to characterize gene function. Among other uses, the collection will allow bioenergy researchers to quickly identify mutations involved in cell wall biosynthesis, critical for increasing plant yields.


Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility and the DOE Joint BioEnergy Institute (contract DE-AC02-05CH11231). This work was also supported by the National Institutes of Health and the National Science Foundation.


G. Li, R. Jain, M. Chern, N.T. Pham, J.A. Martin, T. Wei, W.S. Schackwitz, A.M. Lipzen, P.Q. Duong, K.C. Jones, L. Jiang, D. Ruan, D. Bauer, Y. Peng, K.W. Barry, J. Schmutz, and P.C. Ronald. “The sequences of 1,504 mutants in the model rice variety Kitaake facilitate rapid functional genomic studies.” The Plant Cell (2017). [DOI: 10.1105/tpc.17.00443]

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The University of Utah College of Engineering has received a $2 million grant to create a laboratory and develop new technology for communities with backup power sources, known as microgrids, so they can quickly and more securely operate in the event of a massive power outage due to a natural disaster or cyberattack.

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U.S. Energy Secretary Rick Perry announced that the Department of Energy will award 219 grants totaling $34 million to 183 small businesses in 41 states. Funded through DOE's Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs, today's selections are for Phase I research and development.

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ORNL Facility Receives American Nuclear Society's Historic Landmark Designation

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Steven Cowley named director of DOE's Princeton Plasma Physics Laboratory

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PNNL Part of a New National Center for Near-Atomic Resolution of Biological Molecules

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SLAC Will Open One of Three NIH National Service Centers for Cryo-Electron Microscopy

The National Institutes of Health announced today that it will establish a national service and training center for cryogenic electron microscopy research at the Department of Energy's SLAC National Accelerator Laboratory.

Planck Collaboration Wins 2018 Gruber Cosmology Prize

The Planck Team--including researchers in Lawrence Berkeley National Laboratory's (Berkeley Lab's) Computational Research and Physics divisions--have been awarded the 2018 Gruber Cosmology Prize.

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Powering Up With a Smart Window

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Remnant Superconductivity From Invisible Stripes

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Optimizing lithium-sulfur battery electrolytes for long life.

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New spectroscopic technique measures heat in itty-bitty volumes that could reveal insights for electronics and energy technology.

Water, Water, Everywhere, but How Does It Flow?

Scientists use new X-ray technique to see how water moves at the molecular level.

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