Stem rust discovery solves decades old genomic puzzle

For decades researchers and crop breeders have known that something in wheat’s notoriously complex genome was suppressing the plant’s resistance to the fungal pathogen.

Now with the identification of the underlying genetic mechanism that causes suppression researchers have potentially removed a stubborn barrier to developing crops with stronger immunity using modern genomic tools.

Researchers have shed new light on a longstanding mystery of what makes bread wheat susceptible to the devastating disease stem rust.

For decades researchers and crop breeders have known that something in wheat’s notoriously complex genome was suppressing the plant’s resistance to the fungal pathogen.

Now with the identification of the underlying genetic mechanism that causes suppression researchers have potentially removed a stubborn barrier to developing crops with stronger immunity using modern genomic tools.

Dr. Matthew Moscou of The Sainsbury Laboratory, and one of the lead authors of the study, explains the significance of the findings:

“This is the first identification of a trans-suppressor in wheat meaning that it’s a gene somewhere in the genome that is impairing the function of other genes somewhere else in the genome.

“Our study opens the way to a novel approach at improving agriculture through removal of suppressors that negatively interact in wheat.”

At the heart of the mystery is the notoriously complex bread wheat genome which is composed of three separate genomes A, B and D. These are derived from three different independently evolved grass species. Sometimes these genomes work together producing desirable traits such as bigger seeds. Sometimes they produce negative effects, a phenomenon known as genome conflict.

In the 1960s Canadian researcher Eric Kerber showed that when the D genome was removed, the plant switched from being susceptible to rust to resistant.

Further investigations over 20 years narrowed down the cause of this phenomenon to a gene on a single locus on chromosome 7D that was suppressing the plant’s resistance to stem rust.

Now in this study researchers use modern sequencing techniques, genetic mapping, and mutational analysis to identify the gene that suppresses resistance to stem rust.

Researchers inoculated wheat plants with stem rust and compared the responses to a range of mutant plants that had lost the suppressor gene.

Normally wheat responds to stem rust with around 8,000 genes being expressed. In these tests one mutant responded with around 2,200 genes, another mutant with 55 genes. Critically, these mutant plants are resistant, whereas the parent wheat plant is susceptible.

“The weird thing is that you think the plants responding to the pathogen would be a good thing, it would make it resistant. But in fact, this is the opposite. The plant that is responding is the susceptible one and the one not responding is the resistant one,” explains Dr. Moscou.

The next steps of the research are to identify additional genes that contribute to immune suppression in wheat and to understand how these genes broadly impact the wheat genome.

In addition to identifying the underlying gene the researchers made two unexpected findings:

• The gene discovered here belongs to the Mediator protein complex. This is a conserved mechanism in plants, fungi and animals and orchestrates how and when genes are expressed in the genome
• The researchers identified two regions on different sub-genomes 1A and 1D that are segmentally co-regulated. The regions are huge – encompassing 25 megabases - and there is no known mechanism that could regulate a region of this size in eukaryotes (plants, animals, yeast)

The study: 'Stem rust resistance in wheat is suppressed by a subunit of the Mediator complex', appears in Nature Communications.