A novel genetic process behind the emergence of a deadly wheat disease

Our study for the first time assembles the two haploid nuclear genomes of a dikaryotic fungus and shows that a nuclear exchange event led to the emergence of the devastating wheat stem rust strain Ug99

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Since ancient times, wheat farming has been plagued by rust diseases. Roman farmers made offerings to appeal to the rust god, Robigus, to protect their crops from this devastating disease. Rust diseases are actually caused by fungi of the Pucciniales order, and wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most important diseases of wheat.

Breeding wheat for genetic resistance to stem rust has been pretty successful in preventing major epidemics of this disease in more recent times. Indeed, these achievements contributed to Dr. Norma Borlaug receiving the Nobel Peace Prize in 1970. However, the emergence of a new strain of stem rust in Africa 20 years ago put the global wheat community on high alert. This strain, called Ug99 for its first description in Uganda in 1999 by Zacharias Pretorius, overcame the most widely used and hitherto long-lasting resistance gene in wheat, Sr31, as well as many other previously effective resistance genes.  Since its first detection, Ug99 has spread through Africa and the Middle East causing devastating epidemics and is regarded as one of the greatest threats to wheat production worldwide.

Despite its devastating impact, the origin of Ug99 has remained a mystery for the last 20 years. A common assumption has been that such a uniquely virulent strain must be the result of a sexual cross between different rust strains. However, our team found evidence that Ug99 actually arose by a novel genetic process called somatic hybridization, in which a whole nucleus was exchanged between two different strains. Rust fungi are unusual in that each cell contains two separate and different haploid nuclei, so this somatic hybridization can generate novel genetic combinations without the need for the strains to go through their complex sexual cycle. In fact sexual reproduction requires the presence of another host plant, common barberry, which is absent in most parts of the world.

Our work was initially motivated by a need to improve genome reference resources for Pgt using long read sequencing technology to generate complete genome assemblies for Ug99 and an Australian stem rust isolate, Pgt21, that was originally derived from South Africa. The key insight into the origin of Ug99 came when PhD student Feng Li at the University of Minnesota compared the genome sequences surrounding a known virulence gene and noticed that Pgt21 and Ug99 shared one common haplotype at this locus. From there, CSIRO scientist Narayana Upadhyaya devised an approach to identify sequences common to the two strains and assign them to haplotypes. Together they found that the two isolates share one complete haploid genome that is almost identical in sequence, while the second haplotype in each is quite divergent. A crucial input then came from Benjamin Schwessinger and Jana Sperschneider at the Australian National University, who were able to use a physical DNA crosslinking approach (Hi-C) to show that the shared genome sequences were all derived from a single nucleus of Pgt21 without any recombination. This ruled out a sexual origin for Ug99 and convinced us we were dealing with a case of somatic hybridisation in which a whole nucleus had been exchanged between asexual isolates. 

Back in the 1960s, it was proposed that rusts could hybridise based on laboratory studies in which co-infection with different asexual isolates could sometimes give rise to new isolates with novel phenotypes. However, molecular genetic techniques were not available at the time to confirm the origin of the putative hybrids, and particularly to rule out the potential for spore contamination given propensity of the airborne spores to spread. Nevertheless, these insights have now been substantiated, and we revealed that somatic hybridisation was the mechanism behind the emergence of one of the most devastating P. graminis f. sp. tritici strains, threatening global wheat production and food security.

Photo was provided by Prof. Zacharias Pretorius 


Melania Figueroa

Group Leader, CSIRO