The U.S. Department of Agriculture announced Thursday that it has two preferred options regarding alfalfa genetically modified to resist Monsanto’s weed killer Roundup–that it should either be allowed without restrictions, or allowed with certain geographic and isolation restrictions on seeds and, in some places, on hay.

In analyzing the potential impacts of three proposed alternatives, USDA did not prefer a third option–maintaining the engineered alfalfa’s regulated status.

The impact statement evaluating the controversial Roundup Ready alfalfa is the latest chapter in an ongoing saga that began in 2005 when the USDA’s Animal and Plant Health Inspection Service (APHIS) deregulated it.

Farmers and Center for Food Safety sued, and won a favorable ruling upheld in appellate court that barred GM alfalfa until the government adequately studied whether it could contaminate conventional and organic crops.  Monsanto took the matter to the Supreme Court, which voted 7-1 to lift the ban, but also agreed that an impact statement was required.

Yesterday Monsanto said it is ready to begin planting its GM alfalfa in early 2011.  “This is good news for America’s farmer,” said Steve Welker, Monsanto alfalfa lead, in a news release about the EIS completion.  “Farmers have been waiting a long time for the choice to use Roundup Ready alfalfa and realize the dependable weed control that it offers. We are hopeful of getting a green light in the next 30 to 60 days.”

 Andrew Kimbrell, executive director of Center for Food Safety, indicated the fight isn’t over yet.  “The only option that will protect organic and conventional alfalfa growers and dairies is for the USDA to deny any approval of GE alfalfa,” he said in a news release.  “We are disappointed that the agency has not made this one of its preferred options but are encouraged that it remains an option being considered by the agency.”

In announcing the completion of the impact statement, Secretary of Agriculture Tom Vilsack took a conciliatory tone.

“Our goal with the EIS, first and foremost, is to recognize and consider the many concerns that we have heard from all segments of agriculture,” he said in a news release.  “We are equally committed to finding solutions that support not only the developers and users of biotechnology products, but growers who rely on purity in the non-genetically engineered seed supply.”

Before announcing its preferred options, USDA said it considered plant pest issues as well as broader environmental and economic issues related to the coexistence between genetically engineered, non-genetically engineered, and organic alfalfa production.

Vilsack  acknowledged that “we have seen rapid adoption of biotechnology in agriculture, along with the rise of organic and non-genetically engineered sectors over the last several decades.  While the growth in all these areas is great for agriculture, it has also led, at times, to conflict or, at best, an uneasy coexistence between the different ways of growing crops.

“We need to address these challenges and develop a sensible path forward for strengthening coexistence of all segments of agriculture in our country. All are vital and a part of rural America’s success. All should be able to thrive together.”

Vilsack said that USDA is wiling to work “openly and transparently” with all the stakeholders in the debate. 

USDA said the EIS is not a decision document but only an analysis of the potential environmental and economic impacts of the various alternatives. The final EIS will be available for public review for at least 30 days before USDA announces how it will proceed.

APHIS submits the EIS to the Environmental Protection Agency for publication in the Federal Register, and anticipates that EPA will publish a notice that the final EIS is available for public review on Dec. 23.