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June 12, 2011

Stem rust-free wheat varieties developed

by Paul Voosen

A multinational group of scientists has developed farm-ready wheat resistant to a virulent and devastating plague that has slowly spread from Africa into the Middle East, carrying with it the threat of famine.

Researchers at the International Maize and Wheat Improvement Center (CIMMYT) in Mexico will announce next week that they have developed wheat varieties showing "near immune" resistance to deadly stem rust disease. Once thought as well-conquered as polio, stem rust is known for killing as much as half a harvest.

A mutant strain of the fungus that causes stem rust appeared in Uganda a decade ago, tearing through previously resistant crops. Scientists found that the fungus, Ug99, could infect 90 percent of the world's wheat, causing a surge of concern from the United States to India. Wheat provides a fifth of the world's calories; a mass outbreak risked plunging many societies back into hunger, reversing agriculture's gains in the developing world.

The outlook was grim. Conventional methods of containing the disease failed, most spectacularly several years ago in Kenya, where Ug99 mutants soon overcame an introduced resistance. The fungus spread, appearing in South Africa and Iran. Blowing in the wind, its minute spores dance on the edges of wheat-dependent countries like Egypt and Turkey, threatening their populations with massive crop failure.

Those failures could still come, and the disease is far from conquered. Vigilant tracking is needed. The resistant wheat has not been widely deployed, and it could face bureaucratic or funding hurdles in its African spread. But the wheat, proven to survive heavy disease pressure in Kenya, is the best shot farmers have of stopping stem rust in its tracks, scientists say.

"We need that stuff," said Ronnie Coffman, the head of the Durable Rust Resistance in Wheat project at Cornell University, a $67 million effort funded by the Bill and Melinda Gates Foundation. "This is the major project that we have."

The CIMMYT effort was led by Ravi Singh, a wheat breeder and pathologist mentored by Norman Borlaug, the father of the Green Revolution, who himself first defeated stem rust in Mexico many decades ago. Singh is one of the few remaining experts able to eyeball the shape and spew of a rust pustule and understand the genes underlying the trait, Coffman said.

"If we didn't have what Ravi and his colleagues have put together over the years," Coffman said, "we wouldn't have anything to deploy in the countries in the path of Ug99."

Singh is one of a rare breed. At most some 10 researchers in the world retained expertise in stem rust prior to Ug99, according to Jim Anderson, a wheat breeder at the University of Minnesota. As the disease disappeared from the farm, investment slacked and only a few centers like CIMMYT kept up programs studying the plague.

"It just really wasn't seen as a problem anywhere throughout the world," Anderson said.

Singh will announce the results of his group's work next week at a stem rust workshop in St. Paul, Minn., home to one of only four labs worldwide equipped to study Ug99 and its mutants. (The United States and Canada accept Ug99 only in winter; South Africa and Australia have banned Ug99 imports.) Singh published an advanced description of his team's progress last month in the Annual Review of Phytopathology.

The gains made by Singh's group represent a stark change in how crop disease is tackled, moving away from the boom-and-bust cycles that have long characterized breeding. There were easier paths they could have explored, but their introduced resistance should remain durable, not undermined in a few years, he said.

"We don't want this to be a cat-and-mouse game," Singh said. "This is looking toward a little bit longer term."

The resistant wheat was developed in large part without the advanced molecular tools that have widely penetrated breeding efforts in many labs. It also flies in the face of traditional approaches to resisting disease, which involve crossing single disease-resistance genes into a crop. Singh eschewed this approach, instead breeding up to five "minor" genes into his wheat, an intricate technical feat accomplished at a rapid pace.

Farmers in Ethiopia, who have had to make do with less-than-ideal wheat, are clamoring for the resistant varieties, frustrated with the government's decision to multiply the seed first, Singh said. India has committed to generating 8,000 tons of the seed, while, if USAID financing holds, the crop should be distributed in countries like Nepal, Pakistan, Egypt and Bangladesh.

The final test for the resistant wheat will come over the next couple of years, once farmers sow the crop in volume. While the multiple genes introduced into the wheat should pose an evolutionary conundrum to the Ug99 and its mutants -- it is typically much easier for pests to overcome single genes -- there are no certain bets, said Jorge Dubcovsky, a wheat geneticist at the University of California, Davis.

"The durability of the different genes is something that only time will tell," Dubcovsky said.

Should the resistance hold up, scientists and governments would still face the costly enterprise of spreading the wheat to countries most at risk from Ug99. While regions like Europe have less to fear from stem rust, given their massive reserves of fungicide, it will take Western and local investment to propagate the wheat in Africa and the Middle East, Singh said.

"Developing these resistant varieties does not mean we have won the battle," he said. "These have to be grown by farmers. It still takes effort to put it into the farmer's field."

Many farmers have little desire to replace their crops. Wheat varieties in the developing world are often 10 or 20 years old, and while farmers in Kenya have had painful encounters with stem rust, their peers in Iran, which has not suffered from an outbreak, may be reluctant to change crops. Most will have never encountered stem rust before.

"Farmers get comfortable with certain varieties," said Minnesota's Anderson. "It may have drought resistance or be particularly well adapted to their region. They may have to see it in their neighbor's field."

Conditions vary in each country, from farm regulators down to individual farmers. The public wheat sector is infamous for its bureaucracy and seed release committees, and some of those standards may have to be waived, Coffman said. Plus, some African countries lack the facilities to multiply wheat seeds, let alone cross the immune crops into local varieties.

"It's really important to get the seed out there, but it's an enormous challenge," Coffman said. "It's enormously expensive. You think about what it costs to change all of the wheat varieties in the world. Think of the area."

The push for a durable variant is far from complete. Beyond Singh's group, breeders are focusing on rust-resistant strains based on single genes, which are easier to develop. Singh suspects these single-gene varieties could be deployed in regions unlikely to experience yearly rust outbreaks, while his wheat provides the first line of defense in Africa and the Middle East.

Singh's approach to Ug99 involved overturning an orthodoxy that has been held by much of the breeding community since the Green Revolution and spearheaded by Singh's past mentor, Borlaug.

Breeders have long divided disease-resistance genes into "major" and "minor" categories. Major genes provide resistance individually, allowing breeders relatively cheap and quick methods of developing hardy crops. Minor genes, meanwhile, might slow a disease's grasp without halting it entirely, or may only become effective during maturity. Alone, they make unattractive targets.

Decades ago, wheat breeders chose to focus on major genes, which soon led to spectacular success against stem rust. Borlaug and others discovered, through sheer grinding effort, a gene called Stem Rust 31, or Sr31, which provided complete rust protection. Scientists moved Sr31 into wheat across the world, protecting crops for decades, sparing millions of lives. But finally, in Uganda, Sr31 fell to Ug99.

Many geneticists could have predicted the failure of Sr31. While major genes have many desirable traits, they are vulnerable to mutations: A single switch in a pathogen's DNA can allow it to overcome the genetic defense. For example, there are 70 major genes known to halt stripe rust, another wheat disease, but only three remain widely effective. Since its discovery, six mutants of Ug99 have already appeared, overcoming various major genes.

Scientists have long known that disease resistance based on multiple genes is far more likely to remain durable, as evolution makes it difficult for microbes to simultaneously adapt to two different genes. In the early 1980s, Singh read the work of a Canadian scientist, Doug Knott, who predicted that introducing four or five minor genes into wheat would cause a broad resistance to all varieties of stem rust. He found Knott's conclusions convincing.

Back then, working out among the chaff, Singh could see evidence that major genes were not the only good bet. There were wheat varieties that had resistance no one could explain, he said.

"You start to see things which don't fit to the model," he said.

Until Ug99, though, Singh's interest in minor genes remained largely academic. Seeing the failure of major genes against the fungus, Singh and his collaborators began breeding minor genes into CIMMYT's wheat stocks. The scheme oscillated between field sites in Mexico and Njoro, Kenya, with crops planted twice a year.

Beyond one minor gene, Sr2, little was known about the genes to be targeted, but Singh suspected that Knott's hypothesis would hold true: Four or five minor genes would grant near immunity.

There are few organizations that can match the sheer numbers Singh threw at the problem. Breeding is, at its heart, a game of odds, and getting crops that carry minor genes, along with all the other traits desired by farmers like grain length, requires long odds. And so Singh spread his bets widely, growing about 2 million wheat plants over CIMMYT's many acres.

This is brute-force breeding in classic Borlaug style, Cornell's Coffman said. "The rest of the breeding world is amazed by the numbers that they throw at it," he said. "But it gets results."

By last year, at the end of their first long-term breeding cycle, the team had developed 298 varieties that expressed resistance or near immunity to Ug99 and its variants. Many of these crops grew full and plump, yielding 10 percent more grain than typical, outdated African wheat. Singh hopes this difference will sell many local farmers on making the change.

If the wheat proves durable, it will have secondary effects for the future, too, Singh said. Every acre devoted to developing stem rust resistance is an acre not going to pressing concerns like drought tolerance or lower fertilizer demands, he said. If minor genes lead away from major gene's boom-and-bust disease cycle, it could free up needed intellectual space.

"People should not take for granted that food is guaranteed forever," he said.

But before then, the world will watch and see whether the minor genes hold off the rust.

"You don't know something's going to be durable," Coffman said, "until it endures."

New York Times

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