Scientists have sequenced the majority of the soybean genome, providing an unprecedented look into how this important legume crop converts four critical ingredients–sunlight, water, carbon dioxide and nitrogen–into protein and oil, the basic building blocks for many consumer products.

The research team from 18 federal, state, public and private organizations, including the University of Nebraska-Lincoln, published their research today in the journal Nature.

“Soybean and other legumes play a critical role in global food security and human health and are used in a wide range of products, from tofu, soy flour, meat substitutes and soy milk to soy oil-based printing ink and biodiesel,” said Molly Jahn, USDA Deputy Under Secretary for Research, Education and Economics. “This new information about soybean’s genetic makeup could lead to plants that produce more beans that contain more protein and oil, better adapt to adverse environmental conditions, or are more resistant to diseases.”

This sequencing of the soy genome is the culmination of more than 15 years of collaborative research. The team used a so-called “whole-genome shotgun” (WGS) approach to sequence 85 percent of the 1.1 billion nucleotide base pairs that spell out soy’s entire DNA code. The sequence also provides researchers with a critical reference to use in deciphering the genetics of some 20,000 other legume species.

 Geneticists Randy Shoemaker, Perry Cregan, David Hyten, Steven Cannon and David Grant with USDA’s Agricultural Research Service (ARS) contributed to the Nature paper. Their work involved the creation of genetic markers and the development of the soybean (Glycine max) genetic map that facilitated “anchoring” of the genome sequence to the 20 sets of soybean chromosomes. ARS is USDA’s principal intramural scientific research agency.

The Department of Energy’s Joint Genome Institute; Purdue University at West Lafayette, Ind.; the University of Missouri at Columbia, and the University of Arizona at Tucson also participated in the soybean sequencing project, which was supported by the National Science Foundation and USDA’s National Institute of Food and Agriculture (NIFA). Through federal funding, NIFA invests in science to solve critical issues impacting people’s daily lives and the nation’s future.

According to USDA’s Shoemaker, who is with the ARS Corn Insects and Crop Genetics Research Unit in Ames, Iowa, integrating the new sequence with existing physical and genetic maps of soy will move researchers closer to linking observable physical traits of soy to their associated genes and alleles–alternate versions of genes. Ultimately, this will speed the development of new soybean cultivars offering higher seed yields, increased protein and oil contents, better adaptability and improved disease resistance, particularly to Asian soybean rust (ASR), which threatens America’s $27 billion soy crop.

“Overlaying the sequence onto available maps will expedite identification and orientation of genetic markers such as single nucleotide polymorphisms, which are often located near genes that control agronomically important traits,” Shoemaker said.

Using such markers, soy breeders can rapidly determine which offspring plants have inherited these traits without growing them to maturity, saving time, money and resources.

“We’ve mapped the locales for about 90 important traits affecting soybean growth and development, seed yield, seed protein and oil, and disease resistance, to name but a few,” Shoemaker added. “With this high-quality sequence, we now have access to candidate genes that we’ve never had before, which will enable us to look at their patterns of expression, develop molecular markers to track them in breeding programs, and work with them to determine their function or modify them to improve their function.”

Some key discoveries already gleaned from the whole-genome sequence include the first soybean gene conferring resistance to ASR, which can cause soy losses of 10 to 80 percent; a mutation that could make soybeans easier to digest by producing lower levels of a carbohydrate called stachyose; a mutation for higher levels of production of the enzyme phytase that could enable livestock to absorb more phosphorus from soybean feed so less gets excreted as a potential water contaminant; and 52 genes that orchestrate development of soy plant root nodules, where symbiotic bacteria transform atmospheric nitrogen into a form soy and other crops can use for their growth and development.

“This is a milestone for soybean research and promises to usher in a new era in soybean agronomic improvement,” said co-author Gary Stacey, Director, Center for Sustainable Energy and Associate Director and National Center for Soybean Biotechnology, University of Missouri. “The genome provides a parts list of what it takes to make a soybean plant and, more importantly, helps to identify those genes that are essential for such important agronomic traits as protein and oil content.”

From the sequence analysis, Stacey said that he and his colleagues have identified more than 46,000 genes of which 1,110 are involved in lipid metabolism. “These genes and their associated pathways are the building blocks for soybean oil content and represent targets that can be modified to bolster output and lead to the increase of the use of soybean oil for biodiesel production.”

While biodiesel from soybean oil represents a cleaner, renewable alternative to fossil fuels with desirable properties as a liquid transportation fuel, there simply is not enough oil produced by the plant to be a competitive gasoline on a gallons-of-fuel yield per acre. The availability of the soybean genome may provide some key solutions.

“We can now zero in on the control points governing carbon flow towards protein and oil,” said Tom Clemente, Professor, Center for Biotechnology, Center for Plant Science Innovation at the University of Nebraska, Lincoln. “With the combination of informatics, biochemistry and genetics we can target the development of a soybean with greater than 40 percent oil content.”

The availability of the soybean genome sequence has accelerated other soybean trait discovery efforts as well. For example, researchers have used the sequence to zero in on a mutation that can be used to select for a line that has lower levels of the sugar stachyose, which will improve the ability of animals and humans to digest soybeans.

In another effort, by comparing the genomes of soybean and corn, a single-base pair mutation was found that causes a reduction in phytate production in soybean. Phytate is the form in which phosphorous is stored in plant tissue. Because phytate is not absorbed by the animals that eat the feed, the unabsorbed phytate passes through the gastrointestinal tract, elevating the amount of phosphorus in the manure. Limiting phytate production in the soybean could reduce a major environmental runoff contaminant from swine and poultry waste.

Of additional importance for soybean farmers is that the genome sequence has provided access to the first resistance gene for the devastating disease Asian Soybean Rust (ASR). In countries where ASR is well established, soybean yield losses due to the disease can be as high as 80 percent.

The American Meat Institute (AMI) Friday told the Office of the U.S. Trade Representative that mandatory country-of-origin labeling (COOL) violates the United States’ international trade obligations for many reasons and that the U.S. must honor these obligations. 

 The comments were provided in response to a December 4, 2009, Federal Register Notice.  Canada and Mexico in late 2009 filed a case against the United States with the World Trade Organization (WTO), a move that came as no surprise given those countries’ outspoken opposition to the labeling law when it was under consideration by Congress.

In comments, AMI Senior Vice President of Regulatory Affairs and General Counsel Mark Dopp said that equitable enforcement of international trade rules is a high priority for everyone and that all too often,  market access for U.S. meat products has been threatened or cut off with little or no legitimate justification.

 “American challenges to these actions have been based upon the rights provided under international trade agreements. These challenges will continue, as demonstrated by a recent limitation to an important market for beef.  Critical to the United States’ ability to enforce successfully World Trade Organization (WTO) and North American Free Trade Agreement (NAFTA) obligations is consistency in U.S. behavior and actions,” Dopp said.   “In that regard, the United States’ credibility is undermined when U.S. legislation violates America’s commitments pursuant to those international agreements. In the instant case, the U.S. COOL requirements, as provided for in the 2002 Farm Bill (and modified in the 2008 Farm Bill) and as implemented through regulations that became effective March 16, 2009, are not consistent with U.S. obligations under both WTO and the General Agreement on Tariffs and Trade (“GATT”) and NAFTA.”

 COOL is inconsistent with trade agreements because of its discriminatory effect on imported meat and imported live animals.  The U.S. must ensure that the products of other countries “imported into the territory of [the United States]…be accorded treatment no less favorable than that accorded to like products of [U.S.] origin in respect of all laws…affecting their internal sale.”

 According to Dopp, COOL affects the internal sale of meat derived from foreign animals in the United States by creating notable disadvantages in selling imported foreign meat, as well as selling “foreign” animals to U.S. meat packing facilities.  Significantly, GATT provides that “formal” identical treatment, i.e., that both U.S. and imported products must be marked with the country of origin, does not justify a law such as COOL where that law discriminates against imports in practice. 

 “The result is that COOL is de facto discrimination against foreign products, a result even contemplated by sponsors of the legislation who declared that it would be ‘helpful to a lot of American agricultural producers’ and force companies to rely ‘on our independent producers here in this country,’” according to Dopp.

 COOL also is not consistent with the WTO Agreement on Technical Barriers to Trade (TBT).  The TBT Agreement specifically governs any technical regulation which, like COOL, “deal[s] exclusively with…marking or labeling requirements as they apply to a product.” The TBT Agreement requires that the United States use international standards as the basis for its technical regulations. COOL breaches those U.S. obligations by failing to use two such standards.

 First, the Codex General Standard for the Labeling of Prepackaged Foods provides that “when a food undergoes processing in a second country which changes its nature, the country in which the processing is performed shall be considered to be the country of origin for the purposes of labeling.” COOL does not meet this international standard, Dopp said.  In addition, the Codex General Standard provides that “the country of origin of the food shall be declared if its omission would mislead or deceive the consumer.”  The U.S. Government, however, has never claimed that customers were misled or deceived.

 Second, the WTO Rules of Origin Agreement stipulates that the final harmonization work program must determine a country of origin as “the country where the last substantial transformation has been carried out.”   COOL, however, denies U.S. country of origin to animals and meat products that are substantially transformed in the United States, and thus fails to conform to this international standard, Dopp noted.

COOL also violates the TBT agreement by creating unnecessary obstacles to international trade.  Its non-trade objectives are minimal, and COOL does not have as an objective protecting “human health or safety, animal or plant life or health, or the environment.”

 “Indeed, the U.S. Government has repeatedly stated that COOL ‘is not a food safety or animal health measure. Likewise, COOL is not a ‘national security requirement’ nor does COOL have as its purpose preventing ‘deceptive practices.’ Neither sponsors of the legislation nor U.S. Government agencies have made such a claim,” Dopp said. 

The stated objective of COOL is to provide ‘consumer information,’ but AMS found that the “expected benefits from implementation of this rule are difficult to quantify. In fact, the agency concluded that that the economic benefits will be small and will accrue mainly to those consumers who desire country of origin information and that all available evidence shows that “consumers do not have a strong preference for country of origin labeling.”

 “In a number of cases meat packers have chosen either to cease buying imported livestock – an extreme trade restriction – or have confined the processing of imported livestock to limited dates and times. These practices, in turn, have significantly restricted trade,” Dopp wrote.

 In addition, to be consistent with GATT, COOL must be administered uniformly and reasonably.  But according to Dopp, “COOL applies only to “covered commodities” and not to a host of products such as turkey, processed foods, etc. and, therefore, is not consistent,” he said.   Reasonableness requires that the administration of laws be “proportionate” and “appropriate” and, comparing the significant costs imposed on the U.S. importers and the foreign producers of animals and meat products to the scant legitimate benefit identified by the U.S. government, COOL cannot be deemed to be reasonable.

Sen. Ben Nelson, D-Neb., was one of the 26 U.S. Senators urging strong support from U.S. representatives in defending Country of Origin labeling in WTO complaints.

Sen. Mike Johanns, R-Neb., is not one of the 26 bipartisan coalition of senators urging a defense of COOL legislation.

R-CALF USA CEO Bill Bullard recently met with Edward Avalos, U.S. Department of Agriculture (USDA) Under Secretary for Marketing and Regulatory Programs, other USDA officials and congressional staffers to discuss the country-of-origin labeling (COOL) law and the joint Senate letter circulated by Sen. Tim Johnson, D-S.D., and Sen. Mike Enzi, R-Wyo., which encourages U.S. Agriculture Secretary Tom Vilsack and  U.S. Trade Representative,  Ambassador Ron Kirk, to continue to aggressively defend COOL against the World Trade Organization (WTO) complaints filed by Canada and Mexico, two of this country’s NAFTA partners. 

 “In addition to its support of the joint Senate letter, R-CALF USA reiterated its recommendation that USDA immediately begin a new rulemaking to close the loophole in the COOL law that allows the mislabeling of USA beef with a multi-country label,” said R-CALF USA COOL Committee Chair Mike Schultz.

 Bullard said R-CALF USA said that a new rulemaking may nullify the Canadian and Mexican complaints because these countries would be given an opportunity to express their concerns in the new rulemaking, making the WTO complaint premature.

“We also provided officials with documentation showing that numerous countries that accept U.S. beef exports continue to ban Canadian beef and beef derived from Canadian cattle imported into the United States,” he said. “These export bans help to explain that the reduced demand for Canadian beef and cattle in the U.S. is due in large part to ongoing safety concerns about Canadian beef and are not the result of the COOL law.”   

 The joint Senate letter states in part:

 “Over forty-five other nations have each already implemented a food labeling program which provides country of origin information to consumers.  As you know, both Canada and Mexico have implemented food labeling programs of their own to make such information available.  Some of the origin labeling programs implemented in other countries require that more information be made available to the consumer than what is required by the food labeling program in the United States.  The food labeling programs established to date in other countries clearly indicate that the United States is implementing a reasonable program which is compliant with our trade obligations.”

 An additional 24 Senators, listed below, signed on to the joint Senate letter in support of COOL:  Johnson (D-SD), Enzi (R-WY), Sen. Byron Dorgan, D-N.D.; Sen. John Barrasso, R-Wyo.; Sen. Russ Feingold, D-Wis.; Sen. Max Baucus, D-Mont.; Sen. Lisa Murkowski, R-Ark.; Sen. Jon Tester, D-Mont.; Sen. Tom Harkin, D-Iowa; Sen. Carl, D-Mich.; Sen. Claire McCaskill, D-Mo.; Sen. Dianne Feinstein, D-Calif.; Sen. Kent Conrad, D-N.D.; Sen. John Thune, R-S.D.;  Sen. Herb, D-Wis.; Sen. Richard Shelby, R-Ala.; Sen. Sherrod Brown, D-Ohio; Sen. Olympia Snowe, R-Maine; Sen. Ben Nelson, D-Neb.; Sen. Susan Collins, R-Maine; Sen. Mary Landrieu, D-La.; Sen. Ron Wyden, D-Ore; Sen. Jeff Merkley, D-Ore.; Sen. David Vitter, R-La.; Sen. Amy Klobuchar, D-Minn.; and, Sen. Al Franken, D-Minn.

The Rainwater Basin Joint Venture will host its 15^th annual Informational Seminar on Wednesday, February 3, at the Quality Hotel and Convention Center, 2201 Osborne Drive, in Hastings, Nebraska.

The one-day seminar, from 9:00 to 4:00, is an opportunity for landowners, agriculture producers, natural resource professionals, and other interested individuals to share ideas and learn about conservation issues, research, and habitat programs in south-central Nebraska’s Rainwater Basin region.

 An afternoon panel discussion will address a variety of conservation programs for private land, including the Wetlands Reserve Program, the Wetland Initiative Program, and the Working Landscapes initiative. Other sessions include discussions about the role of wetlands in protecting water quality; management of vegetation in Rainwater Basin wetlands; and the benefits of filling unused irrigation pits. In addition, throughout the day Rainwater Basin landowners who have participated in Joint Venture projects and other wetland programs will discuss their experiences.

The seminar is open to the general public. Agenda details are at www.rwbjv.org.

To register, please send an e-mail by January 26, to Shanda Weber at shanda.weber@ne.usda.gov; include name, organization, and mailing address. Or phone 402-463-6771 ext. 112. A $20 registration fee, payable at the door, covers all sessions, snacks, and a buffet lunch. Landowners and agriculture producers in the Rainwater Basin are invited to register free of charge.

 The Informational Seminar is funded in part by a grant from the Nebraska Environmental Trust.

The Rainwater Basin Joint Venture is a public-private partnership created through the North American Waterfowl Management Plan. It is composed of conservation agencies, local government bodies, non-profit organizations, and individuals, each contributing their expertise and resources to the protection and restoration of wetland habitat in south-central Nebraska’s Rainwater Basin region.