Fighting rust fungal crop threats through integrated genomics research

Posted on 06.02.2017 | Last Modified 22.02.2021
Lead Researcher (PI): Guus Bakkeren
Institution: Agriculture & Agri-Food Canada
Total WGRF Funding: $199,000
Co-Funders: Alberta Wheat Commission
Start Date: 2015
Project Length: 4 Years

To understand the mechanism by which pathogenic rust fungi cause disease, and vice versa, by which host plants mount defences, in order to design novel methods to introduce more durable disease resistance into into Canadian crops.

Project Summary:

Rust diseases are a serious threat to the Canadian wheat crops. To increase genetic and other forms of resistance in wheat plants is the most economical way to prevent damage by these fungal pathogens, including less reliance on chemical pesticides. Wheat suffers from damage caused by three rusts in the genus Puccinia: leaf, stem and stripe rust, whereby in Western Canada, especially the latter has become a serious problem. For some of these rust diseases, a fairly good level of genetic resistance exists in current wheat varieties, but these fungal pathogens have a marked propensity to mutate and overcome such resistances, necessitating continuous breeding efforts to introduce new resistance genes.
Genomics research on the rust pathogens has advanced enormously over the last 10 years, and has increased our understanding of how variable their genomes are and how specific small proteins (effectors) produced by the fungi are crucial as virulence factors to infect the host and cause disease. Some effectors interact with the wheat resistance proteins that prevent the fungus from causing disease. The mutation ability and variation of these effectors lies at the root of breaking resistances in the wheat host. This project made use of genomics technologies to generate whole genome sequences of 65 Canadian leaf rust fungus isolates, which together with 30 previously generated genomes and 55 from the USA, yielded insights into the genetic variation in North-America. This allowed a comprehensive list of over 1,100 potential effectors and their variants to be compiled, a crucial resource to find interacting wheat resistance genes, using a developed effector function screening tool.
Among many, three fungal pathogenicity genes were identified in the genomic resources for utilization in the Host-Induced Gene Silencing (HIGS) technology we adapted to combat cereal rusts. In this technology, these fungal genes are silencing targets and portions of those gene sequences were expressed in double-stranded RNA form from loci embedded in wheat cultivar Fielder. These proved to be stable inherited traits that can suppress rust fungus development in the wheat host once they infect. This proof-of-concept research was shown to enable increased rust disease resistance in an otherwise susceptible wheat cultivar. This is a novel way to achieve increased resistance in this pathosystem and the loci developed can be introduced in any elite wheat cultivar (if amenable to genetic transformation).
Towards the establishment of a (fungal) cereal disease monitoring network, automated air-borne spore collectors gathered weekly samples over four growing seasons at three pilot sites in BC and five in AB. Upon a national survey among pathologists and extension workers, we focused on six wheat pathogen species deemed of most importance to Western Canadian growers: the three Puccinia rusts, Fusarium Head Blight, powdery mildew species, and several cereal leaf spot diseases caused by Pyrenophora species. Using literature data and our own research, we developed and/or optimized DNA-based diagnostic PCR (Polymerase Chain Reaction) assays for these pathogens. Using these, samples from AB were shown in these small-scale pilots to reveal seasonal trends of varied presence of these fungal pathogens in different locations. The samples from BC were analyzed using a metagenomic sequencing approach: through next-generation sequencing of the diagnostic ribosomal region in the fungal genomes, and the use of a computational pipeline and extensive databases, we generated a comprehensive picture of all fungal species in the traps and hence produced and present in the respective regions, over four growing seasons (2015 – 2018). Several of the target cereal pathogens were present and are being verified with the developed diagnostic assays. The data will be analyzed using a climatic / weather model to assess the predictability of (cereal) diseases. It is anticipated that the overall concept employed in this project will be expanded to become a nationwide “Phytoshield”, which aims at developing and incorporating fast reliable molecular assays for pathogen monitoring with predictive value for rust fungi and other fungal crop diseases of economic importance. This would be one of the pillars of the envisaged “Biovigilence” program for Canada. The current assays can potentially be commercialized