Ug99 stem rust, a devastating wheat fungus, has spread south. Credit: Cereal Disease Lab / USDA

Two new forms of a devastating wheat fungus, known as Ug99 stem rust, have shown up in South Africa, a study has found.

The two South African forms are able to overcome the effects of two resistance genes in wheat that normally prevent stem rust from taking hold. The genes cause plant cells around the infection site to die, stopping the fungus from further infecting the plant. They are two of the most important genes in wheat because they are selected for in crop-breeding programmes across the world. The discovery of the new forms marks the first time that the stem rust fungus with virulence against key genetic resistance has moved south of its origins in Uganda, east Africa, the research says.

The presence of new forms of Ug99 in South Africa makes wheat crops in areas including the Middle East and south Asia vulnerable as the fungus can now migrate using different wind trajectories, says Zacharias Pretorius, a wheat pathologist at the University of the Free State in Bloemfontein, South Africa, and one of the authors of the study. Pretorius and his colleagues will present their research in early June at a conference on wheat rust in St Petersburg, Russia, organized by the Borlaug Global Rust Initiative, which was founded by the late US agronomist Norman Borlaug, winner of the 1970 Nobel Peace Prize.

It's mutating and migrating. ,

"It's mutating and migrating," says Pretorius. "The concern is that other wheat-growing countries will become vulnerable to infection."

"Eventually it will reach North America and Europe," says Ronnie Coffman, a plant-breeding scientist at Cornell University in Ithaca, New York. He warns that in the next few years, farmers across the world will need to replace up to 90% of the current wheat varieties with new, resistant varieties to ensure crops are protected against the fungus.

Arms race

The reddish-brown, wind-borne fungus was first discovered in Uganda in 1999 and has since spread to five countries, including Kenya, Ethiopia and Iran. It attacks the stems of wheat plants by destroying vascular tissue so that plants can no longer stand upright. Infected plants produce fewer seeds and may die. The fungus can devastate harvests: for example, farmers in the Narok region of Kenya lost up to 80% of their wheat crop due to Ug99 in 2007.

In total, seven mutant strains of the fungus are now known, including the latest forms, originally identified in South Africa in 2007 and 2009. These strains pose an even greater threat to wheat than other types of Ug99 because they are more virulent and the wheat plants have fewer defences against infection, says Pretorius.

Pretorius and his team analysed the genomes of the new stem rust variants and compared them to the genome of a common and less dangerous form of the fungus found in South Africa in 2000. The team found that the variant detected in 2007 is likely to have arisen through a single mutation of the more common form, making it able to overcome the Sr24 wheat gene that usually confers resistance to the pathogen. The team also found that the variant discovered in 2009 was likely to have migrated into South Africa from another country in east Africa, such as Kenya, and is able to overcome the effects of the resistance gene Sr31 as well as Sr24.

The fungus and its variants are now able to overcome at least 32 of around 50 resistance genes, according to Ravi Singh, a plant geneticist and pathologist at the Mexico-based International Maize and Wheat Improvement Centre.

An international project that is researching resistance to wheat rust, led by Cornell University, is developing new tools to help defeat the pathogen. Sarah Davidson, associate director of the project, says that it will have isolated eight new resistance genes by the end of the year. The project is also investigating why rice, the only cereal that is not damaged by the rust, is immune.