U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Mutant Rice Database for Bioenergy Research
Published: June 01, 2017
Posted: September 01, 2017

Genome-wide distribution of fast neutron-induced mutations in the Kitaake rice mutant population. [Image courtesy of Guotian Li and Rashmi Jain]

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

The Science
Researchers produced a database of mutations in an important grass crop: rice. They used fast-neutron irradiation, a process that efficiently induces a wide variety of genetic mutations through exposure to high-energy neutrons. After irradiating the plants, they resequenced 1,504 mutants and identified structural variants and mutations. The results provide an invaluable resource for grass models being used to improve candidate bioenergy feedstock crops such as switchgrass.

The Impact
Boosting yields of bioenergy feedstock crops such as grasses requires a better understanding of how enzymes and proteins synthesize plant cell walls in order to modify the processes and the composition. The team’s goal is to have a functional genomics resource for grass models involved in plant cell wall biosynthesis studies. Until now, mutant collections for grass models have lagged behind those available for the Arabidopsis 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. A team led by University of California, Davis, and including 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, have assembled the first major large-scale collection of mutations for grass models. 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, 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.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy

Kent Peters, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of

PI Contact
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute

Pamela Ronald
University of California, Davis

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 number DE-AC02-05CH11231). This work was also supported by the National Institutes of Health (NIH) and the National Science Foundation (NSF).

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.17.00154]  (Epub ahead of print) (Reference link)

Related Links
Berkeley Lab News Release: A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks
Berkeley Lab News Release:  Plant Cell Highlight: “Technology Turbocharges Functional Genomics”
KitBase (Kitaake Rice Mutant Database)
Crop Genetics Innovation
Pilot Study: Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation
Nipponbare/japonica subspecies of Oryza sativa on Phytozome
JBEI Feedstocks Division
Grasses: The Secrets Behind Their Stomatal Success

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Plant Systems and Feedstocks, Plant-Microbe Interactions
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: DOE Bioenergy Research Centers (BRC)

Division: SC-23.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

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