Net tightens around wheat's ancient nemesis

Dr Evans Lagudah

Dr Evans Lagudah: No gene works in isolation – they
need to talk to each other.

The time frames required to progress from identifying an interesting wheat trait to isolating the underlying gene are getting shorter if rust resistance research is anything to go by.

When Dr Evans Lagudah at CSIRO Plant Industry cloned Lr34 in 2009 it took almost a decade, and even that time frame was extraordinary given the sheer volume and complexity of the bread wheat genome.

But it took just half that time to get the first-ever example of an actual stem rust resistance gene, an event that coincided with the isolation of another stem rust resistance gene in the US.

Of the two genes, Sr33 was cloned in Australia from the goatgrass genome (Aegilops tauschii), a wild relative that is the progenitor of bread wheat’s D genome (one of three genomes that cohabitate in bread wheat and originate from different progenitor wheat species). 

The clue to the existence of Sr33 first came to light in the 1970s when Canadian geneticist Dr Eric Kerber hybridised an Iranian goatgrass line with durum. The resulting synthetic wheats were found to possess broad-spectrum stem rust resistance that has fascinated molecular biologists – including Dr Lagudah – ever since.

To isolate Sr33, the CSIRO team worked with rust specialists at the University of Sydney Plant Breeding Institute in Cobbitty and molecular biologists in the US and China. The project also received vital funding over many years from the GRDC and the Australian Centre for International Agricultural Research (ACIAR).

Dr Lagudah says that on its own, Sr33 provides only intermediate levels of protection, but it provides this for all stem rust races tested, including Ug99.

Then this level of resistance provided by Sr33 can be boosted when combined with other resistance genes. This includes a resistance gene called Sr2, which is already common in many Australian wheat varieties.

“No gene works in isolation – they need to talk to each other,” Dr Lagudah explains.

“We want to create an informed, knowledge-based approach as to which genes you should combine to obtain the most effective and durable forms of rust resistance. So cloning genes such as Sr33 is a vital stepping stone to that agronomically important end.”

Previously, Dr Lagudah and his CSIRO team isolated Lr34, a remarkable gene that provides partial resistance to all leaf and stripe rust races tested while also boosting the effects of certain stem rust resistance genes. The discovery of Lr34 was reported in the May–June 2009 issue of Ground Cover.

Photo of Dr Sam Periyannan

Dr Sam Periyannan: from a poor smallholder farm in
India to being a key member of an Australian rust
research team that has just made one of the most
significant advances towards combating this ancient
nemesis of grain growers everywhere.

PHOTO: Brad Collis

“We are interested in genes such as Lr34 and Sr33 from the point of view that they provide resistance to many different rust races,” Dr Lagudah says. “That is an interesting attribute to understand at the molecular level. Another is how well Sr33 and Sr35 complement each other. If we can better understand attributes like this, it can really help us stay ahead of rust disease.”

In a particularly apt twist, the gene’s isolation – and its food security effects – owes much to two poor, smallholder crop growers in southern India, Kuppusamy Periyannan and his wife Subhulakshmi.

They took out loans against their 1.3-hectare farm to educate their children and insistently pushed one, Sambasivam (‘Sam’) Periyannan, to forgo engineering in favour of studying agricultural science. Their son Sam was subsequently responsible for cloning Sr33 at the CSIRO laboratory while completing his PhD from the University of Sydney on an ACIAR scholarship.

Dr Periyannan has since stayed on at CSIRO as a postdoctoral fellow and is now closing in on two other novel stem rust resistance genes as part of the Borlaug Global Rust Initiative and the GRDC’s Triple Rust Initiative.

“My parents see science as an aid to farming, so it was that background which pushed me to try and excel at agricultural research,” Dr Periyannan says.

“When I started my PhD it was a time when Norman Borlaug put out a food security alarm pointing to the threat from rust disease to world wheat production. So I feel proud that something from this work goes back to growers, including smallholders, which is where my own roots are.”

The second gene, Sr35, was isolated in the US by a team led by Professor Jorge Dubcovsky from the University of California, Davis, and Associate Professor Eduard Akhunov of Kansas State University.

Unlike the Australian gene, Sr35 provides strong levels of resistance, but the resistance is restricted to a subset of stem rust races that include the Ug99 race group.  Similar strategies were used to isolate the genes – a feat that Dr Lagudah compares with finding two tiny needles in a very large haystack. However, Sr35 was not sourced from goatgrass but from the genome of one of the earliest cultivated forms of wheat – einkorn (Triticum monococcum), the progenitor of bread wheat’s A genome.

“Since the 1950s, wheat breeders were able to develop varieties that are largely resistant to stem rust, so for decades this disease wasn’t the biggest concern,” Associate Professor Akhunov says.

“However, the emergence of strain Ug99 in Uganda in 1999 devastated crops and has spread to Kenya, Ethiopia, Sudan and Yemen. It shows that changes in the virulence of existing races can become a huge problem.”

The world has scrambled ever since to build up wheat’s defences against Ug99, with breeders at the International Maize and Wheat Improvement Center on the front line, releasing resistant material to affected nations.


  • For the first time, Australian and US research teams
    have isolated stem rust resistance genes
  • The genes, effective against Ug99, are “underexploited”
    in cultivated bread wheat
  • The discovery has brought new insights into resistance and is
    driving new advances in molecular breeding technologies

The cloned genes add to those defences and provide ‘perfect markers’ to ease selection of the associated resistance. However, Dr Lagudah warns that Sr33 should never be deployed in cultivated varieties on its own in order to prevent the breakdown of its valuable broad spectrum form of resistance. 

“Isolating the genes also means we can start building DNA cassettes with selected combinations of the most useful forms of resistance – and possibly other valuable traits like tolerance to saline soils,” Dr Lagudah says, referring to the salt-tolerance genes also isolated at CSIRO with GRDC support.

“The cassette can then be inserted into one site in the wheat genome allowing all the genes to be inherited together, and simply, in every generation. It then takes just one marker to select for the entire cluster, clearing the way for breeders to focus their crosses on combining beneficial yield and quality traits.”

Another technology that the genes make possible is under development at CSIRO by Dr Peter Dodds and involves recycling resistance into genes that have fallen over due to the emergence of novel rust races. This technology was the subject of a Ground Cover feature in the July–August 2008 issue.

More information:

Dr Evans Lagudah,



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GRDC Project Code CSP00099

Region National, Overseas