Genome-wide rice studies yield first major, large-scale collection of mutations for grass models.
Fast-neutron irradiation, exposure to high energy neutrons, induces a wide variety of mutations by making changes in DNA. Using this approach, rice researchers were able to create the first major, large-scale collection of mutations for grass models. Resequencing the 1,504 mutants has allowed researchers to identify structural variants and mutations, providing an invaluable resource for grass models being used to improve candidate bioenergy feedstock crops such as switchgrass.
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. Information on this new, large-scale collection of more than 90,000 mutations affecting nearly 60 percent of all rice genes is available on a publicly accessible database called KitBase. This comprehensive resource could help identify rice lines with mutations in specific genes and to characterize gene function. The UC Davis team is seeking assistance for seed distribution efforts – contact lead investigator Pam Ronald.
Daniel Drell, Ph.D.
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Plant Program Head
DOE Joint Genome Institute
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.17.00443 [Epub ahead of print]
- Berkeley Lab News Release: A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks
- 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