Wheat’s rust resistance hidden in the genes

A seed collection gathered by a little known Englishman in the 1920s and ‘30s is opening up new possibilities for Australian scientists breeding disease resistant wheat varieties.

Google the name Arthur Ernest Watkins and there is scarcely a mention of the man who gathered a geographically and genetically diverse collection of wheat seeds from across the vast British colonial empire.

But it is this collection, housed at the Australian Winter Cereals Collection in Tamworth, NSW, that scientists at the Australian Cereal Rust Control Program (ACRCP) have turned to for new sources of naturally occurring disease resistance.

Rust diseases cause massive economic and yield losses globally. In Australia alone stripe rust has been estimated to cost industry $127 million a year, leaf rust $12m and stem rust $8m a year.

And while some wheat varieties are more resistant to these diseases than others, the disease pathotypes vary from country to country; can be transferred across the globe; and have the ability to mutate into new forms against which popular wheat varieties may be susceptible.

The counter to this immense problem is in the genes and one of the great strengths of wheat as a plant species is its genetic diversity.

There are 30 genera, plus dozens of species within the tribe of grasses that are also related to wheat. These wild relatives had to be tough to survive, and evolved to thrive in the most adverse environments.

But the Green Revolution of the mid 20th century put the focus on breeding for yield, which left many wild relatives, as well as traditional varieties, on the sidelines as the major breeding programs focussed on producing lines shorter in stature but higher in grain load.

Now wheat breeders are returning to wheat’s genetic diversity in the hope of finding new genes that show resistance to the many and varied rust pathotypes which cripple crops around the world, and can be combined with modern high quality varieties.

And so it is that ACRCP scientists Associate Professor Harbans Bariana and Dr Urmil Bansal have been sourcing seed from the Watkins Collection and scoring these lines against Australian and foreign strains of stem rust, stripe rust and leaf rust pathogens with promising results.

Their work involves identifying the genes responsible for resistance in different wheat varieties and how they respond to various strains of the different rust diseases.

Assoc. Prof. Bariana said some of the lines tested from the Watkins Collection have shown wide resistance against Australian rust pathotypes, with a number of lines already identified that provide both seedling (overall) and adult plant resistance (APR).

As a result, the genetically linked genes Lr52 and Yr47, found in a line in the Watkins Collection originally gathered from Iran, are now being bred into modern high-quality Australian wheat varieties to provide both leaf rust and stripe rust resistance. This line also carries a gene for stem rust resistance against Ug99, a widely devastating pathotype of the stem rust pathogen.

"We are now crossing these lines with Australian germplasm because this gene is not present in current Australian wheats,” Assoc. Prof Bariana said. “Within the next 18 months we will be giving breeders this gene bred into Australian genetic backgrounds for use in commercial breeding programs.”

The Australian Cereal Rust Control Program (ACRCP - formerly known as National Wheat Rust Control program, National Cereal Control program) – was established in 1973 and is now funded largely by the grains industry through the Grains Research and Development Corporation (GRDC). The ACRCP program is led by GRDC Chair of Cereal Rust Research, Sydney University Professor Robert Park, and brings together scientists from the University of Adelaide, University of Sydney, CSIRO, and the International Centre for Wheat and Maize Improvement (CIMMYT) in Mexico. The program is also actively involved in the Borlaug Global Rust Initiative.

The GRDC believes that international collaboration will ensure Australian breeders can access the most appropriate sources of genetic material available. The GRDC alone invested $22 million in 2009-10 in wheat and barley pre-breeding programs aimed at identifying novel genes and delivering germplasm to breeding companies with improved drought, frost and salinity tolerance and improved disease resistance.

Assoc. Prof. Bariana said this joint approach, together with collaboration between Australian research bodies, also ensured that the genes identified as part of the ACRCP’s disease resistance program fitted in with the broader industry variety goals.

The ACRCP provides plant breeders with the opportunity to screen their breeding populations under artificially created epidemics using commercially important rust pathotypes, which have been collected and stored at Sydney University since the 1920s.

For their part Assoc. Prof. Bariana and Dr Bansal are not only testing the performance of wheats of various genetic backgrounds against these rust pathotypes, but are also working to identify and map the locations of new genes and then back-cross these genes into common, high-quality Australian wheat varieties.

"We have to get those genes from relatively poor quality wheats into high quality lines through the process of backcrossing, and then that material is delivered to breeding companies for diversifying their sources of resistance,” Assoc. Prof. Bariana said.

"The breeding companies then either release new varieties out of that material or they use those lines as rust-resistant donors for their breeding programs.”

And while a number of stem rust, stripe rust and leaf rust resistance genes have been identified by the ACRCP team, the ultimate goal is to breed new wheat varieties carrying not just one rust-resistant gene, but stacked with combinations of genes carrying resistance to a multitude of pathotypes of all three major rust diseases.

"We’re trying to achieve the pre-breeding objectives of diversifying combinations of resistance genes to all three rust diseases in the germplasm which is fed to the breeding companies here in Australia,” Assoc. Prof. Bariana said.

To achieve this, the team is using a combination of phenotypic data – based on observations of which plants perform best under disease pressure – and the DNA marker technology.

Having identified the best sources of resistance, Dr Bansal then works on finding the chromosomal location of the genes to prove their uniqueness.

This mapping process involves first identifying which chromosome is carrying the resistance gene or genes. Then, using DNA marker technology, Dr Bansal narrows the search by identifying as many known DNA markers as possible on that chromosome.

As part of this process, Dr Bansal searches for genetic linkages between rust resistance gene and DNA markers that can ultimately aid in tracing the target resistance in breeding populations. This should indicate that wherever the linked markers are present, the disease resistance gene should also be present.

In the event of failure to find a single marker that is linked with the target resistance gene, one marker on each side of and as close as possible to the resistant gene can also be used for indirect selection of resistance genes. This process allows breeders to combine two or more genes that can be traced through their linkage with DNA markers.

Having identified and located resistance genes, the plant populations carrying those genes are then scored for their levels of resistance – some genes providing minor levels of resistance to certain pathotypes, while other genes are highly resistant.

"We want to make sure that new wheat lines are protected preferably by combinations of minor (APR-adult plant resistance gene) genes and/or combinations of both major (overall) and minor rust resistance genes,” Assoc. Prof. Bariana said.

"By combining the phenotypic data from the field or greenhouse and the genotypic information from the lab we can be doubly sure that we can combine different type of genes. The positive DNA fingerprints for the resistance genes can assure their presence in the target germplasm.”

And while not all new gene combinations are compatible, there has been a significant progress. For example, the ACRCP team found that northern variety Sunco and southern variety Kukri both carried three different adult plant stripe rust-resistance genes.

These have now been inter-crossed to produce new triple-rust-resistant hybrids – some comprising 75 per cent Sunco for northern conditions and some made up of 75pc Kukri for southern conditions – with all carrying between four to six genes for stripe rust resistance, two to three genes for leaf rust resistance, and possessing different combinations of stem rust resistance genes Sr2, Sr24, Sr30, and Sr36.

"That material was delivered to breeding companies about three years ago, which they are now using as rust resistant donor sources in their breeding programs,” Assoc. Prof. Bariana said.

Source: GRDC (Grains Research & Development Corporation)