The announcement was made by Eddy Rubin, DOE JGI Director, during his keynote remarks Jan. 15 at the Plant and Animal Genome XVI Conference in San Diego,CA. The preliminary data can be accessed at http://www.phytozome.net/soybean.
The soybean genome project was initiated through the DOE JGI Community Sequencing Program (CSP) by a consortium led by DOE JGI’s Dan Rokhsar, Stanford’s Jeremy Schmutz, Gary Stacey of the University of Missouri-Columbia, Randy Shoemaker of Iowa State University, and Scott Jackson of Purdue University, with support from the U.S. Department of Agriculture and the National Science Foundation.
The large-scale shotgun DNA sequencing project began in the middle of 2006 and will be completed in 2008. A total of about 13 million shotgun reads have been produced and deposited in the National Center for Biotechnology Information (NCBI) Trace Archive in accordance with the consortium’s commitment to early access and consistent with the Fort Lauderdale genome data release policy.
The current assembly (representing 7.23x coverage), gene, set, and browser are collectively referred to as "Glyma0". Glyma0 is a preliminary release, based on a partial dataset. This is expected to be replaced with an improved, chromosome-scale "Glyma1" version by the end of 2008. Early users of this data are encouraged to track their favorite genes by saving local copies of the DNA sequences of these loci, and not by identifier or sequence coordinate, as these will change in future versions.
DOE JGI’s interest in sequencing the soybean stems from its role as a principal source of biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel.
Detailed knowledge of the soybean genetic code will enable crop improvements for more effective application of this plant for clean bioenergy generation. Knowing which genes control specific traits, researchers are able to change the type, quantity, and/or location of oil produced by the crop. Through utilization of the sequence information generated by DOE JGI, it may be possible to develop a customized biomass production platform for combining oil seed production for biodiesel with enhanced vegetative growth for ethanol conversion--doubling the energy output of the crop. In 2004, over 3.1 billion bushels of soybeans were grown on nearly 75 million acres in the US, with an estimated annual value exceeding $17 billio--second only to corn, and about twice that of wheat.
Several other individuals, projects, grants, and agencies have made this monumental project possible. These included the four major projects: Public Expressed Sequence Tags (ESTs), SoyMap (which includes BAC libraries, modern physical mapping, and clone-based sequencing), and the Genetic Map with funding from USDA, NSF, United Soybean Board (USB), and the North Central Soybean Research Program (NCSRP).
The Public EST Project, supported by USB and NCSRP, was led by Lila Vodkin of the University of Illinois at Urbana-Champaign; Randy Shoemaker of the USDA-ARS, Ames, Iowa; and P. Steven Keim of Northern Arizona University.
The original physical map development, funded by USB, was conducted by Jan Dvorak, from the University of California, Davis, along with the Washington University Genome Center in St. Louis, Missouri, and David Grant, USDA-ARS, Ames, Iowa.
The NSF SoyMap team, comprising principal investigator Scott Jackson, Gary Stacey and Henry Nguyen, Jeff Doyle of Cornell University, William Beavis of the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico, and Iowa State, Gregory May (NCGR), Will Nelson and Rod Wing of the University of Arizona, with Randy Shoemaker, anchored the map and conducted quality control.
The team devoted to genetic mapping and physical map anchoring, yielding several thousand sequence-based markers, included USDA-Agricultural Research Service (ARS) investigators, including Perry Cregan and Dave Hyten of Beltsville, Maryland; Randy Shoemaker, David Grant, and Steven Cannon of USDA-ARS Ames, Iowa; along with James Specht of the University of Nebraska, Lincoln.
The annotation of the soybean genome was carried out by a team of researchers from the DOE JGI and the University of California Berkeley’s Center for Integrative Genomics, with support from the DOE, USDA, NSF, and the Gordon and Betty Moore Foundation.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
David Gilbert | EurekAlert!
High-precision magnetic field sensing
05.12.2016 | ETH Zurich
Energy hybrid: Battery meets super capacitor
01.12.2016 | Technische Universität Graz
Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.
The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...
Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water
In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
05.12.2016 | Power and Electrical Engineering
05.12.2016 | Information Technology
05.12.2016 | Earth Sciences