Doe Science news source
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.

Summary

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.

Funding

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.

Publications

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]

X
X
X
  • Filters

  • × Clear Filters

Breakthrough Cuttable, Flexible, Submersible and Ballistic-Tested Lithium-ion Battery Offers New Paradigm of Safety and Performance

Breakthrough Cuttable, Flexible, Submersible and Ballistic-Tested Lithium-ion Battery Offers New Paradigm of Safety and Performance

Chemical Treatment Improves Quantum Dot Lasers

One of the secrets to making tiny laser devices such as opthalmic surgery scalpels work even more efficiently is the use of tiny semiconductor particles, called quantum dots. In new research at Los Alamos National Laboratory's Nanotech Team, the ~nanometer-sized dots are being doctored, or "doped," with additional electrons, a treatment that nudges the dots ever closer to producing the desired laser light with less stimulation and energy loss.

Neutrons Observe Vitamin B6-Dependent Enzyme Activity Useful for Drug Development

Scientists at the Department of Energy's Oak Ridge National Laboratory have performed neutron structural analysis of a vitamin B6-dependent protein, potentially opening avenues for new antibiotics and drugs to battle diseases such as drug-resistant tuberculosis, malaria and diabetes. Specifically, the team used neutron crystallography to study the location of hydrogen atoms in aspartate aminotransferase, or AAT, an enzyme vital to the metabolism of certain amino acids.

Scientists Decode the Origin of Universe's Heavy Elements in the Light From a Neutron Star Merger

On Aug. 17, scientists around the globe were treated to near-simultaneous observations by separate instruments that would ultimately be confirmed as the first measurement of the merger of two neutron stars and its explosive aftermath.

PPPL Takes Detailed Look at 2-D Structure of Turbulence in Tokamaks

Article describes study of cross-correlation of turbulence in tokamaks.

New Method to Detect Spin Current in Quantum Materials Unlocks Potential for Alternative Electronics

A new method that precisely measures the mysterious behavior and magnetic properties of electrons flowing across the surface of quantum materials could open a path to next-generation electronics. A team of scientists has developed an innovative microscopy technique to detect the spin of electrons in topological insulators, a new kind of quantum material that could be used in applications such as spintronics and quantum computing.

Purple Power: Synthetic 'Purple Membranes' Transform Sunlight to Hydrogen Fuel

Argonne researchers have found a new way to produce solar fuels by developing "synthetic purple membranes." These membranes involve an assembly of lipid nanodiscs, man-made proteins, and semiconducting nanoparticles that, when taken together, can transform sunlight into hydrogen fuel.

Sandia Researchers Use Direct Numerical Simulations to Enhance Combustion Efficiency and Reduce Pollution in Diesel Engines

A "cool flame" may sound contradictory, but it's an important element of diesel combustion -- one that, once properly understood, could enable better engine designs with higher efficiency and fewer emissions.

Converting Carbon Dioxide to Carbon Monoxide Using Water, Electricity

Researchers at the University of Illinois at Chicago and the Joint Center for Artificial Photosynthesis have determined how electrocatalysts can convert carbon dioxide to carbon monoxide using water and electricity. The discovery can lead to the development of efficient electrocatalysts for large scale production of synthesis gas -- a mixture of carbon monoxide and hydrogen.

International Team Reconstructs Nanoscale Virus Features from Correlations of Scattered X-rays

Berkeley Lab researchers contributed key algorithms which helped scientists achieve a goal first proposed more than 40 years ago - using angular correlations of X-ray snapshots from non-crystalline molecules to determine the 3D structure of important biological objects.


  • Filters

  • × Clear Filters

LIGO Announces Detection of Gravitational Waves From Colliding Neutron Stars

The U.S.-based Laser Interferometer Gravitational-Wave Observatory and the Virgo detector in Italy announced on Oct. 16 that all three of their detectors had picked up the ripples, or gravitational waves, from two neutron stars that collided 130 million years ago. Among other discoveries, the detection allowed scientists to use gravitational waves to directly calculate the rate at which the universe is expanding.

WVU Energy Conference to Address State's Economic Opportunities

West Virginia University will look at the state's emerging energy economy through industry experts, public policy organizations, environmental groups and academic institutions at the sixth annual National Energy Conference Oct. 20.

Exploring the Exotic World of Quarks and Gluons at the Dawn of the Exascale

As nuclear physicists delve ever deeper into the heart of matter, they require the tools to reveal the next layer of nature's secrets. Nowhere is that more true than in computational nuclear physics. A new research effort led by theorists at DOE's Thomas Jefferson National Accelerator Facility (Jefferson Lab) is now preparing for the next big leap forward in their studies thanks to funding under the 2017 SciDAC Awards for Computational Nuclear Physics.

Matthew Latimer Receives 2017 Lytle Award

A staff member at the Department of Energy's SLAC National Acceleratory Laboratory, Matthew Latimer is in charge of seven spectroscopy beamlines at SSRL. He was recently selected for the 2017 Farrel W. Lytle Award, established by the SSRL Users' Organization Executive Committee. The award promotes accomplishments in synchrotron science and supports collaboration among visiting scientists and staff who conduct research at SSRL.

Jefferson Lab Completes 12 GeV Upgrade

Nuclear physicists are now poised to embark on a new journey of discovery into the fundamental building blocks of the nucleus of the atom. The completion of the 12 GeV Upgrade Project of the Continuous Electron Beam Accelerator Facility (CEBAF) at the Department of Energy's Thomas Jefferson National Accelerator Facility (Jefferson Lab) heralds this new era to image nuclei at their deepest level.

Sunderrajan to Lead Science and Technology Partnerships and Outreach Directorate

Suresh Sunderrajan has been named the associate laboratory director (ALD) for the Science and Technology Partnerships and Outreach (STPO) Directorate at the U.S. Department of Energy's Argonne National Laboratory.

Career Awards Advance Research for Jefferson Lab Researchers

Two researchers affiliated with the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility have received 2017 Early Career Research Program awards from the DOE's Office of Science.

U.S. Department of Energy Awards Danforth Center $16M to Enhance Sorghum for Bioenergy

This project aims to deliver stress-tolerant sorghum lines, addressing DOE's mission in the generation of renewable energy resources.

Four Los Alamos Scientists Named as 2017 Laboratory Fellows

Four Los Alamos National Laboratory scientists have been named 2017 Fellows.

Creation of New Financial Product Aims to Solve "Valley of Death" for Promising Energy Technologies

With a DOE grant, two professors will create a new investment tool to manage risk and catalyze funding at critical stages for energy companies


  • Filters

  • × Clear Filters

Discovering the Genetic Timekeepers in Bioenergy Crops

A new class of plant-specific genes required for flowering control in temperate grasses is found.

New Technology Illuminates Microbial Dark Matter

Demonstrating the microfluidic-based, mini-metagenomics approach on samples from hot springs shows how scientists can delve into microbes that can't be cultivated in a laboratory.

Tiny Green Algae Reveal Large Genomic Variation

First complete picture of genetic variations in a natural algal population could help explain how environmental changes affect global carbon cycles.

A Complex Little Alga that Lives by the Sea

The genetic material of Porphyra umbilicalis reveals the mechanisms by which it thrives in the stressful intertidal zone at the edge of the ocean.

Precise Radioactivity Measurements: A Controversy Settled

Simultaneous measurements of x-rays and gamma rays emitted in radioactive nuclear decays show that the vacancy left by an electron's departure, not the atomic structure, influences whether gamma rays are released.

OLYMPUS Experiment Sheds Light on Inner Workings of Protons

Seven-year study explains how packets of light are exchanged when protons meet electrons.

Explorations of the Universal Glue

The newly upgraded CEBAF Accelerator opens door to strong force studies.

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.

Bringing Visual "Magic" to Light

Scientists create widely controllable ultrathin optical components that allow virtual objects to be projected in real environments.

Speeding Materials Discovery Puts Solar Fuels on the Fast Track to Commercial Viability

In just two years, a process that was developed by Molecular Foundry staff and users has nearly doubled the number of materials with the potential for using sunlight to produce fuel.


Spotlight

Tuesday October 03, 2017, 01:05 PM

Stairway to Science

Argonne National Laboratory

Thursday September 28, 2017, 12:05 PM

After-School Energy Rush

Argonne National Laboratory

Thursday September 28, 2017, 10:05 AM

Bringing Diversity Into Computational Science Through Student Outreach

Brookhaven National Laboratory

Thursday September 21, 2017, 03:05 PM

From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

SLAC National Accelerator Laboratory

Thursday September 07, 2017, 02:05 PM

Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

SLAC National Accelerator Laboratory

Thursday August 31, 2017, 05:05 PM

Binghamton University Opens $70 Million Smart Energy Building

Binghamton University, State University of New York

Wednesday August 23, 2017, 05:05 PM

Widening Horizons for High Schoolers with Code

Argonne National Laboratory

Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

Rensselaer Polytechnic Institute (RPI)

Wednesday September 16, 2009, 10:00 AM

College Presidents Flock to D.C., Urge Senate to Pass Clean Energy Bill

National Wildlife Federation (NWF)

Wednesday July 01, 2009, 04:15 PM

Northeastern Announces New Professional Master's in Energy Systems

Northeastern University

Friday October 12, 2007, 09:35 AM

Kansas Rural Schools To Receive Wind Turbines

Kansas State University

Thursday August 17, 2006, 05:30 PM

High Gas Prices Here to Stay, Says Engineering Professor

Rowan University





Showing results

0-4 Of 2215