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!
A big nano boost for solar cells
18.01.2017 | Kyoto University and Osaka Gas effort doubles current efficiencies
Multiregional brain on a chip
16.01.2017 | Harvard John A. Paulson School of Engineering and Applied Sciences
An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...
Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...
Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.
While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...
Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales
Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...
Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.
As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...
19.01.2017 | Event News
10.01.2017 | Event News
09.01.2017 | Event News
20.01.2017 | Awards Funding
20.01.2017 | Materials Sciences
20.01.2017 | Life Sciences