Minnesota researchers take on deadly fungus threatening world’s wheat crop

Yue Jin
MinnPost photo by Sharon Schmickle
Yue Jin, of the USDA’s Cereal Disease Lab in St. Paul, examines a stalk of wheat.

GREAT RIFT VALLEY, KENYA — A virulent new version of the deadly fungus stem rust is ravaging wheat in Kenya and spreading beyond Africa to threaten one of the world’s most important food crops.

The urgency of the threat is not lost on crop scientists in American Midwest. In the 1950s, stem rust destroyed half of the wheat crop in North Dakota and Minnesota and slashed yields elsewhere throughout North America’s Great Plains.

That crisis and others like it prompted scientists to create resistant varieties that have filled breadbaskets worldwide ever since.

Now, the killer farmers thought they had defeated 50 years ago is back with a vengeance. It surfaced in East Africa in 1999, jumped the Red Sea to Yemen in 2006 and turned up this year in Iran where it endangers much of Asia.

Scientists are powerless to stop its spread and frustrated in their rush to find resistant plants. The disaster unfolding in Kenya could erupt anywhere the rust spores settle.

Once established, stem rust can explode to crisis proportions within a year under the right weather conditions, said Norman Borlaug, who deployed techniques he had learned at the University of Minnesota to lead the fight against stem rust in the 20th century. He won a Nobel Peace Prize for saving millions from hunger.

“This is a dangerous problem because a good share of the world’s area sown to wheat is susceptible to it,” Borlaug said. “It has immense destructive potential.”

Joseph Atrono knows the full measure of its destructive power. His wheat field, on a ridge overlooking the Rift Valley, is a pathetic tangle of broken stems topped by empty hulls where grain should have formed.

Along with the crop went the income Atrono needed to feed his wife and four children.

Now, a few scrawny chickens pecking at the dirt outside his mud-and-stick house are his last defense against hunger. Atrono is selling hens one by one to keep beans in the pot his barefoot wife, Sally Rono, stews over a wood fire.

“I keep asking myself what I will do when the hens are gone,” Atrono said. “Where will I get the income to feed my family?”

Genetic barrier shattered
Coming on the heels of tight grain supplies and food riots last year, the budding rust epidemic exposes the fragility of the food supply in poor countries. It is a grim reminder that the ever increasing global population is vulnerable to pathogens that inevitably surface somewhere on Earth.

Wheat is a major source of calories and nutrition worldwide. In the half century since scientists bred new resistance into wheat by adding genes that stood up to rust, more than 1 billion people in developing countries have come to count on it for food and income.

Now, that genetic barrier is shattered, said Robert McIntosh, former director of Australia’s rust control program.


Audio/slide show about deadly fungus threatening Kenya’s wheat crop.

This “new and dangerous” version of rust “has the potential to migrate to a huge area of wheat extending from Eastern Africa, through the Middle East, potentially to Europe and across to India,” McIntosh said.

E-mail alarm
The first signal of impending danger came in an email in 1999 to Ravi Singh, a wheat expert at the International Maize Wheat Improvement Center (CIMMYT) in Mexico.

A scientist who had trained under Singh was reporting findings from field trials in Uganda. Singh could not believe what he saw: Plants that were bred to resist stem rust had succumbed to the fungal parasite.

“It was shocking,” Singh said. “We had never seen such susceptibility. . . .The first thing you think is that it probably is not true.”

Laboratories in South Africa and Minnesota discovered why it was true. In the biological churn that constantly endows old pests with new genetic combinations, stem rust had acquired a frightening ability to punch through the resistance that had guarded wheat for decades.

Eighty percent of Asian and African wheat varieties are susceptible. So is barley.

The name given to this new menace was UG99 for its discovery in Uganda in 1999. Scientists say it probably started earlier in Kenya where more wheat is grown.

History of destruction
Stem rust has robbed farmers of their harvests since the Bronze Age.

“This is the disease that caused the great plagues of biblical times,” said Ronnie Coffman, an international professor of plant breeding at Cornell University.

In modern times, a stem rust epidemic in the United States set off worries that there would not be enough grain to feed Allied troops fighting World War I.

An outbreak anywhere is a threat everywhere because stem rust spores are notorious for their ability to hitch rides — on the wind, clothing and other transport — and travel for thousands of miles.

In March, the Food and Agriculture Organization of the United Nations warned Afghanistan, India, Pakistan, Turkmenistan, Uzbekistan and Kazakhstan to be on high alert for the disease. In India alone, more than 50 million farmers are at risk.

Unlike common rust infestations that reduce yields somewhere on Earth every year, stem rust can topple a whole field. 

“It can take everything,” McIntosh said. “It is the most damaging of the rusts.”

Better-off farmers can spray fungicides to salvage at least some of their crops. That’s what Geoff and Luke Nightingale — a father-son team farming a few miles from Atrono — did when stem rust attacked their 1,350 acres of wheat.

“Everything got stem rust and it went down fast,” Luke said. “We sprayed twice in three weeks, once by tractor and once by plane.”

Still, Geoff called the yields “terrible, awful.”

Small-scale farmers
Throughout the developing world, hundreds of millions of small-scale farmers like Atrono are the most vulnerable.

Atrono spent most of his 35 years working for others and saving for the day when he could farm on his own. He saw his chance last year when wheat prices skyrocketed because supplies were tight. Wheat typically thrives here in the fertile Rift Valley where contours of green hills mark the horizon until it fades into a distant haze.

So in June Atrono rented two acres of land, bought seed and planted his family’s dreams along with the crop. The seeds worked their magic, and the field was a model display in the dazzling green of young grass.

“When I looked at it, I felt so good,” Atrono said.

Three of his four sons would be going to school in the fall, and there would be money for clothes and shoes as well as for expanding his plantings next year.

What Atrono couldn’t see was the parasitic fungus that was latching onto the stems and hijacking nutrients that should have fed the growth of grain.

Even when Atrono did see powdery, rust-colored blisters, he couldn’t afford enough fungicide. So the rust ran unrestrained.

Now he has no grain to harvest. He plans to chop the barren stalks in hopes of selling them for forage and using the cash to plant beans and potatoes his family could eat in a few months.

In all, Atrono estimates he lost 25,000 Kenyan Shillings (more than $300) plus his labor since June. Before the farming venture, the family was living and saving small sums on 70,000 shillings a year.

“Now I have nothing,” he said.

The story was the same all along the ridge where Atrono farms.

Joseph Kangogo plans to harvest what he can from his 10 acres of wheat and use the cash to buy corn meal to feed his six children. They have no choice but to give up their occasional meal of beef.

“I spent the last of my cash spraying the plants,” said Kangogo who is 47. “This is the worst crop I have seen in my lifetime and I have farmed all of my life.”

Another farmer, Peter Njoroge, 33, is begging everyone he knows for loans.

“I’m asking friends to lend me money so I can come up [with a crop] again next year, god will,” Njoroge said.

Mobilizing for battle
Like firefighters responding to an alarm, wheat experts from around the world have mobilized to fight the rust. Ground Zero is the Kenya Agricultural Research Institute’s station near the village Njoro.

Borlaug is among the big-name crop scientists who came. The Kenyans took him to nearby Narok where farmers from the Maasai tribe were losing crops to stem rust.

“I was scared by what I saw because I knew it could spread to big regions,” Borlaug, 94, said in a telephone interview from his home in Dallas.

Only a few living scientists have seen a stem rust epidemic. And only a few farmers understood its devastating potential. It was their grandfathers’ scourge, something they had heard about but never witnessed.

Borlaug needed no history lesson. He threw his considerable clout into recruiting scientists from the world’s major wheat producing countries and raising funds to underwrite their work.

Major foundations in the United States and Japan pitched into the effort as did the governments in Canada, India and the United States, Singh said. This year, the Bill and Melinda Gates Foundation awarded $26.8 million to a project led by Cornell with a good share of the research done in Minnesota.

Genetic ammunition
A key first step was to comb the world’s wheat and barley for resistant plants. They could provide genetic ammunition to beat back the rust. 

At Njoro, researchers planted seeds the scientists had sent, then exposed the plants to UG99. It was a high-stakes showdown between UG99 and the planet’s toughest stands of wheat.

In most plots, the grain took a severe beating. 

Yann Manes, a French wheat breeder who also works in Mexico, stripped the head on a typical plant and harvested a handful of chaff. No grain.

“You get this in India on 20 million hectares, and you will see the effects on world markets,” he said.

Yue Jin, a plant pathologist with the U.S. Department of Agriculture’s lab at the University of Minnesota, sorted through rows of the wheat American farmers trust to guard against stem rust. Some that resisted UG99 during trials in 2005 and 2006 were blistered and sickly this year. He suspected UG99 had mutated or else recombined its genes through stem rust’s complex reproduction cycle.

UG99’s persistence tells the scientists they can’t rely on resistance they find in a single variety. Instead, they hope to build a pyramid of resistance drawn from the genes of several different plants.

The long fight
Scientists have found some promising resistance here and there.

But that is “the very, very beginning of a process that can take 10 to 12 years,” said Brian Steffenson, a plant pathologist from the University of Minnesota who was part of the research team in Kenya.

Wheat around the world is an intricate mosaic of subtly different plants that farmers have localized over the centuries to meet conditions in their particular fields. So defeating UG99 is not as simple as identifying one resistant variety and distributing it to farmers. Resistance will need to be bred into every local frame on the mosaic.

Further, resistance alone could be worthless. Farmers also need high yields and other traits. Some farmers specialize in wheat that will make the crustiest of French breads. Others serve cravings for tender pastas, crunchy cereals or sprinkles of bulgar on salads.

Plant breeders must shuffle more than 40 traits when they introduce something new in wheat, Steffenson said. The process involves several generations of cross breeding.

Further complicating the process is the intricate nature of UG99. It can live on barberry bushes when wheat isn’t available.

“To know what is going on in the wheat, we need to know what is happening elsewhere,” said Jin.

So, while working in Kenya in October, Jin followed elephant trails at the foothills of Mount Kenya looking for infested barberry.

Jin also gathered samples of UG99 in Kenya and shipped them through biologically secure channels to USDA’s Cereal Disease Laboratory in St. Paul and another lab in Winnipeg.

Brutal winters in Minnesota and Manitoba will add an extra layer of biosecurity during the analysis because spores of the fungus couldn’t survive the cold if they escaped from the laboratories. Stem rust that devastated Upper Midwestern crops in the 20th century typically wintered further south then rode the wind north in the spring.      

Time unknown
While scientists talk in urgent tones, they have no choice but to proceed in measured, methodical steps.    

How much time do they have before large-scale disaster strikes outside Kenya?

At CIMMYT in Mexico, Singh gets frequent calls from grain traders asking that question. A precise answer could be worth a fortune in grain futures markets.

But there is no reliable answer, Singh said.

“You cannot predict a rust epidemic,” he said. “It depends on too many factors.”

Wind, the timing of rainfall and a myriad of other factors play into the fate of the fungus.

“All of these puzzle pieces have to come together to give you a major epidemic,” Singh said.

Sharon Schmickle writes about national and foreign affairs and science. She can be reached at sschmickle [at] minnpost [dot] com.

The Washington Post published a version of this article.

Travel for this article was supported by the Pulitzer Center on Crisis Reporting. Related blog items and photos can be found on the Pulitzer Web site.

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Comments (1)

  1. Submitted by dan buechler on 02/20/2009 - 12:56 pm.

    This is truly important good stuff. The stuff of headlines not the Oscar race etc. I’m glad you got the Washington Post to run this piece. Congrats!

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