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About half of America's sugar comes from sugar beets, and farmers who grow them are in a bind. That's because a federal court has ruled that they cannot plant genetically engineered varieties next year.

As NPR's Dan Charles reports, many of those farmers say they can't go back to the way they used to work. They don't have the tools or enough conventional seeds.

DAN CHARLES: Almost all sugar beet farmers switched over to so-called Roundup Ready beets two years ago. Those beets can survive doses of the weed killer Roundup, so the farmers can use that chemical on their fields. The farmers did not expect legal problems. After all, Roundup Ready soybeans and corn already cover millions of acres, and biotech beets have received exactly the same government approval.

But they encountered a new line of argument from environmental lawyers like George Kimbrell at the Center for Food Safety.

Mr. GEORGE KIMBRELL (Staff Attorney, Center for Food Safety): The concern is the farmers' loss of their fundamental right to choose the crop of their choice, number one.

CHARLES: An organic farmer might lose that choice, Kimbrell says, if somebody across the road grows genetically engineered versions of the same crop. When the crops flower, they'll cross-pollinate and suddenly the organic farmer has something different.

Mr. KIMBRELL: For example, if you're marketing your product as organic or non-GMO and it's contaminated, you can lose your markets, you can lose your organic certification.

CHARLES: Kimbrell's group, along with some organic seed producers, sued the Department of Agriculture, saying that the USDA didn't look carefully enough at the potential impact of cross-pollination before it approved genetically engineered sugar beets.

And a federal judge agreed. Last month, he shocked the industry by revoking approval of the beets until the USDA carries out an environmental impact study.

That could take a couple of years. So unless there's a new legal twist, next spring, farmers will go back to planting conventional beets, except some of them say they can't.

Mr. DUANE GRANT (Chairman of the Board, Snake River Sugar Company): We're in a little bit of a box, really.

CHARLES: Duane Grant is chairman of the Snake River Sugar Company in Idaho. He says it starts with the most basic thing - the seeds.

Mr. GRANT: The seed companies are telling our company that we don't have enough to plant a full crop in 2011.

CHARLES: And it won't be easy to go back to the old ways of killing weeds - the pre-Roundup methods. The migrant workers who chopped out weeds by hand in the old days don't come through anymore. Grant says he has discarded the special equipment he once used to spray a cocktail of different weed killers every week or so alongside young beet plants.

Mr. GRANT: I simply do not have the expertise on my staff to apply conventional herbicides today. We would have to go back to a training process. I'd have to purchase new sprayers, new cultivators.

CHARLES: Grant is hoping - actually expecting - the USDA to rescue him. There's speculation the agency may issue some sort of interim approval for a Roundup Ready crop next spring. Agency officials declined to comment.

But two weeks ago, the USDA announced it would allow sugar beet seed companies to grow genetically engineered seedlings this fall. Environmental groups immediately sued to block that approval.

Andrew Kimbrell from the Center for Food Safety doesn't have much sympathy for the farmers.

Mr. ANDREW KIMBRELL (Executive Director, Center for Food Safety): They've been on notice since we filed our complaint that this was a likely result of the case - so for over two years now. And so any crying wolf at this point, I think, is not in good faith.

CHARLES: Sugar beet growers in Idaho, like Duane Grant, may be in the worst shape. They fell hardest for biotech beets because they have some of the biggest weed problems. Farmers in other areas, such as the Red River Valley of North Dakota and Minnesota, say they probably could harvest a conventional crop next year. But they warn it will be smaller, and there may be sugar shortages down the road.

Dan Charles, NPR News, Washington.

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