The annual sugar beet harvest is in full swing. Half of the sugar produced in the U.S. comes from beets, and about a quarter of the nation's beets are grown in the West.

A decade ago, Monsanto Company developed a sugar beet that was genetically engineered to survive its Roundup weed killer. But, thanks to public outrage over the prospect of genetically modified candy bars, the GMO beets were put on hold, and the nation's M&Ms and Kit Kats remained GMO-free.

Today, however, Americans consume GMO sweets all the time. Some 95 percent of U.S. sugar beets are Roundup Ready, developed and planted largely under the public radar since the U.S. Department of Agriculture quietly "deregulated" the crop in 2005.

On Sept. 21, though, a U.S. district judge in California hobbled the Roundup Ready revolution when he ruled that the Department of Agriculture broke federal law by approving those beets without fully assessing their environmental impacts.

What happens next is unclear, but a lot of farmers are worried. Judge Jeffrey White has ordered the Department of Agriculture to complete an environmental impact statement, or EIS, on the biotech beets. His decision mirrors another one, issued by the federal 9th Circuit Court two years ago, that required an EIS for Roundup Ready alfalfa -- and prohibited planting it in the meantime. Suddenly, genetically modified crops are receiving more scrutiny than ever before.

When Monsanto first got into genetic modification, the company concentrated on heavyweight commodity crops. In 1996, it introduced Roundup Ready soybeans, followed by cotton and canola in 1997, and corn in 1998. Then Monsanto turned its attention to more specialized crops like alfalfa and sugar beets.

But that effort hit a rough spot in 2001. In response to consumer concern, The Hershey Company and Mars asked farmers not to grow biotech beets "until," as Hershey spokesman John Long told the Wall Street Journal, "the issue related to public perception of GM crops has been fully resolved."

The issue never really got resolved. "As far as we were concerned, (sugar beets) were D.O.A.," says Zelig Golden, a staff attorney for the Center for Food Safety, which filed both the alfalfa and sugar beet lawsuits. "Everyone thought the story was over."

But for many sugar beet farmers -- who cooperatively own the 23 beet-sugar refineries in the U.S. -- biotech beets couldn't arrive soon enough. Duane Grant, the chairman of the Snake River Sugar Cooperative, grows about 6,000 acres of sugar beets near Rupert, Idaho. In the old days, he says, it "was just a real fight to get the beets out of the weeds." A typical season required about 15 separate passes with a tractor, including as many as six to spray a variety of weed killers, capped with a final pass by migrant farmworkers who would hand-hoe the fields.

In 2005, the USDA "deregulated" Roundup Ready beets, clearing them for commercial planting. The decision largely escaped the notice of consumer advocates, but Grant says that beet cooperatives began notifying their wholesale customers "that we were looking at transitioning to biotechnology." (Hershey's and Mars did not respond to attempts to contact them for this story.)

The transition was a fast one. Roundup Ready beets were first planted commercially in 2006. By 2008, Monsanto estimates, roughly half the U.S. sugar beets were Roundup Ready. This year, it's around 95 percent.

About 304,000 acres of sugar beets are being grown in Western states. Idaho ranks first with 164,000 acres, followed by Montana, Colorado and Wyoming; beets are also grown in California and Oregon. The Roundup Ready crop has transformed the way he farms, Grant says. He can "go in and till. Plant. Spray two times. And harvest. It's the most effective method of controlling predatory weeds that we've ever had."

So far, at least. Farmers in the South and Midwest, working with more established Roundup Ready crops such as soybeans and cotton, report that weeds there are now becoming Roundup resistant.