Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers look to relatives for clues in quest to develop sources of bioenergy

15.05.2012
Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle except you don’t have the box and have no idea what the picture is supposed to be.

Sometimes clues from other publicly-available DNA sequences of related organisms can be used to guide the assembly process, but its usefulness depends on how closely related any two sequences are to one another.

For example, a reference genome might be so distantly related from the one being assembled, it would be akin to comparing a Model-T to a contemporary hybrid car.

Nature Biotechnology “Reference genome sequence of the model plant Setaria”.

For researchers interested in switchgrass, a perennial grass that the U.S. Department of Energy (DOE) is investigating as a prospective biofuels feedstock, assembling the plant genome poses an even more complicated puzzle than usual because it has multiple copies of its chromosomes. The genome of a close switchgrass relative, foxtail millet (Setaria italica), is described in the May 13, 2012 edition of Nature Biotechnology “Reference genome sequence of the model plant Setaria”.

For Dr. Tom Brutnell, a co-author on the study and director of the Enterprise Institute for Renewable Fuels at the Donald Danforth Plant Center, the Setaria genome is the starting point for his own research interests. “Now that we have the genome sequence, we can kick start the development of genetic tools for Setaria.” His proposal under the DOE JGI’s 2012 Community Sequencing Program builds off the availability of two Setaria genomes, that of foxtail millet and its wild ancestor green foxtail (S. viridis), which is also described in the paper. “What we really want is an Arabidopsis for the Panicoid grasses,” he said, referring to the ubiquitous model plant used by many researchers. “Green foxtail is smaller than foxtail millet—we can get it to flower when it’s just six inches tall and you go from seed to seed in six to eight weeks. In contrast, foxtail millet is a proper crop so it’s taller, has a longer generation time of four months and no one has really developed efficient transformation methods for it. Our project with the DOE JGI allows us to tap the Setaria genomes to fast track S. viridis as a model genetic system.”

One of the challenges in studying grasses for bioenergy applications is that they typically have long lifecycles and complex genomes. Jeremy Schmutz, head of the DOE JGI Plant Program at the HudsonAlpha Institute of Biotechnology, pointed out that foxtail millet (Setaria italica) has several advantages as a model. It’s a compact genome and large quantities of it can be grown in small spaces in just a few months.

“We’re not thinking of Setaria as a biofuel crop per se but as a very informative model since its genome is so structurally close to switchgrass,” said Jeff Bennetzen, a BESC researcher, the study’s co-first author and a professor at the University of Georgia. He originally proposed that the DOE JGI sequence the foxtail millet genome under the 2008 Community Sequencing Program. Schmutz said that roughly 80 percent of the foxtail millet genome has been assembled using the tried-and-true Sanger sequencing platform, along with more than 95 percent of the gene space—the functional regions of the genome. “The Setaria genome is a high quality reference genome,” he said. “If you want to conduct functional studies that require knowing all the genes and how they are localized relative to one another, then use this genome.”

One such area of study is adaptation. Since it is found all over the world, Setaria is considered a good model for learning how grasses can adapt and thrive under various environmental conditions. Additionally it appears to have independently evolved a pathway for photosynthesis that is separate from that used by maize and sorghum. “With the sequencing of the Setaria genome,” the team noted in their paper, “evolutionary geneticists now have an annual, temperate, C4, drought- and cold-tolerant grass that they can comprehensively compare to other plants that have or have not yet evolved these adaptions.” C4 plants are distinguished by their ability to conduct photosynthesis faster than C3 plants under high light intensity and high temperatures.

The DOE JGI Plant Program focuses on genomes that have been selected for their relevance to DOE missions in energy and environment, and leads the world in sequencing plants in this area. Aside from foxtail millet and switchgrass, other DOE Plant Flagship genomes sequenced include, among others, poplar and soybean. Several of these Flagship genomes are also part of the Gene Atlas project, currently in its pilot phase. Designed to be a reference by which researchers can look up the gene information gathered under several standard experimental conditions, the Gene Atlas is projected to offer researchers a method of interpreting their data by comparing them against “normal” results for these plants. New public releases of these Flagship genomes and of other plant projects occur periodically, and the sequence and analysis is made public at www.phytozome.net.

About The Donald Danforth Plant Science Center

Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research at the Danforth Center will feed the hungry and improve human health, preserve and renew the environment, and enhance the St. Louis region and Missouri as a world center for plant science. The Center’s work is funded through competitive grants and contract revenue from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation, U.S. Department of Agriculture, U.S. Agency for International Development, the Bill & Melinda Gates Foundation and Howard G. Buffett Foundation.

The Donald Danforth Plant Science Center invites you to visit its website, www.danforthcenter.org, featuring interactive information on the Center scientists, news, education outreach and “Roots & Shoots” blog help keep visitors up to date with Center’s current operations and areas of research.

For additional information, contact:

Karla Roeber, (314) 587-1231
kroeber@danforthcenter.org
Melanie Bernds, (314) 587-1647
mbernds@danforthcenter.org

Melanie Bernds | EurekAlert!
Further information:
http://www.danforthcenter.org

More articles from Life Sciences:

nachricht Newly designed molecule binds nitrogen
23.02.2018 | Julius-Maximilians-Universität Würzburg

nachricht Atomic Design by Water
23.02.2018 | Max-Planck-Institut für Eisenforschung GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Good vibrations feel the force

A group of researchers led by Andrea Cavalleri at the Max Planck Institute for Structure and Dynamics of Matter (MPSD) in Hamburg has demonstrated a new method enabling precise measurements of the interatomic forces that hold crystalline solids together. The paper Probing the Interatomic Potential of Solids by Strong-Field Nonlinear Phononics, published online in Nature, explains how a terahertz-frequency laser pulse can drive very large deformations of the crystal.

By measuring the highly unusual atomic trajectories under extreme electromagnetic transients, the MPSD group could reconstruct how rigid the atomic bonds are...

Im Focus: Developing reliable quantum computers

International research team makes important step on the path to solving certification problems

Quantum computers may one day solve algorithmic problems which even the biggest supercomputers today can’t manage. But how do you test a quantum computer to...

Im Focus: In best circles: First integrated circuit from self-assembled polymer

For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.

In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...

Im Focus: Demonstration of a single molecule piezoelectric effect

Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale

Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...

Im Focus: Hybrid optics bring color imaging using ultrathin metalenses into focus

For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.

But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on High Temperature Shape Memory Alloys (HTSMAs)

15.02.2018 | Event News

Aachen DC Grid Summit 2018

13.02.2018 | Event News

How Global Climate Policy Can Learn from the Energy Transition

12.02.2018 | Event News

 
Latest News

A Keen Sense for Molecules

23.02.2018 | Physics and Astronomy

“Laser Technology Live” at the AKL’18 International Laser Technology Congress in Aachen

23.02.2018 | Trade Fair News

Newly designed molecule binds nitrogen

23.02.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>