Maximizing the potential for sustainable and durable resistance to the wheat yellow rust pathogen

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics


Context of the research
Wheat provides approximately 20% of the calories and protein we consume each day and is a major staple across much of the developing world. As the world population continues to increase, the sustainability of wheat yields must be improved by minimizing losses produced by pathogens. Wheat yellow rust, caused by the fungus Puccinia striiformis (Pst), was recently dubbed one of "wheat's worst enemies" and continues to be a major threat to global food security. This disease is an historical and continuing threat to wheat production, capable of significant reductions in both grain quality and yield in susceptible varieties. The appearance of new and more aggressive Pst strains at the beginning of the 21st century and their rapid spread pose an increasing global threat to wheat production, and have resulted in severe yield losses in recent years.
The most economic and environmentally sustainable way to fight yellow rust is by developing wheat varieties that are genetically resistant to the disease. To date, scientist and breeders have deployed resistance genes into agriculture, but with little or no knowledge as to how the pathogen will adapt or respond to them. This inherently 'blind' and inefficient approach has meant that few genes have remained effective in controlling the disease over time. Basically our lack of knowledge of the pathogen's biology and characteristics has meant that we've been fighting with one hand tied behind our backs.

Aims and objectives
Recent innovations in sequencing technologies, combined with increased knowledge of pathogens in other species, provide us with the unprecedented opportunity to start understanding what makes yellow rust such a devastating disease. We propose to use these new technologies to access the complete DNA sequence of multiple strains of the yellow rust pathogen. We will sequence the most current Pst strains from Africa, India and the UK and also go back in time by sequencing historic collections of yellow rust. These strains, which until now have been stored in the cold, tell the story of how the pathogen has changed in history to become more aggressive and overcome wheat varieties that were thought at the time to be resistant. Sequencing will allow us to identify these changes at the DNA level. Understanding and interpreting these changes will provide the context of how wheat varieties and the fungus have co-evolved across three continents. This information will constitute a very powerful framework to identify wheat genes that will stand a better chance at maintaining their resistance against yellow rust in the future. We will use this knowledge to characterize and introduce new sources of yellow rust resistance into modern wheat varieties which are adapted to the different environments. Through this work, we also seek to create new partnerships between researchers and enhance the scientific capabilities of all partners.

Potential applications and benefits
This project will provide insight into how the wheat yellow rust pathogen has evolved to overcome previously effective wheat resistance genes and use this information to develop more sustainable strategies for the future. We will work with local breeders to deploy these new resistance genes which will lead to the development of locally adapted wheat varieties with improved potential to maintain resistance in farmers' fields. These improved varieties will have profound implications from a social, economic and environmental perspective. These varieties should improve the sustainability of food crop production systems and contribute to the alleviation of hunger and poverty of small-holder farmers by reducing the risk of crop failure, increasing profit margins, reducing fungicide applications, protecting yield, and extending the life of varieties which farmers have adopted. These varieties should ultimately translate into increased food security and opportunities to improve farmer income.

Technical Summary

Wheat provides 20% of the calories consumed by humankind and is a major staple across Africa and Asia. Wheat yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide and the appearance of new and more aggressive races has resulted in severe yield losses in recent years. The most sustainable strategy to manage yellow rust is to breed broad-spectrum disease resistance into wheat. To date, resistance genes have been identified, bred, and deployed in agriculture without detailed knowledge of the effectors they are sensing, an inherently 'blind' and inefficient approach. Central to the development of more effective breeding strategies is a better understanding of Pst pathogenicity, virulence factors, and their evolution. However, progress in these areas has been slow and hampered by the lack of Pst genome sequence information. The overall aim of this proposal is to understand the molecular basis of Pst pathogenicity and exploit this information to design effective breeding strategies that maximize the potential for durable disease resistance in the field. The objectives of this proposal are to:
1. Establish a Pst population genomics platform
2. Characterize the pathogenicity arsenal of Pst
3. Evaluate Triticeae germplasm for Pst resistance
4. Fine map and deploy resistance genes which maximize potential for durable resistance
5. Develop and enhance scientific capabilities of Southern partners

This project will provide insight into how the wheat yellow rust pathogen has overcome previously effective R genes, identify and catalogue the effector repertoires of Pst, and identify closely linked markers for R genes with potential for durable resistance. This will lead to the development of locally adapted wheat varieties with improved potential to express durable resistance in the field, improving the sustainability of food crop production systems for small holder farmers.

Planned Impact

The most important impact of this research is the molecular understanding of the pathogenicity of the wheat yellow rust fungus, Puccinia striiformis (Pst); the identification and genetic characterization of resistance sources with broad spectrum recognition specificities; and the deployment of these resistances into high value breeding lines using tightly linked genetic markers. This project will lead to the development of locally adapted wheat varieties with improved potential to express durable resistance in the field compared to traditional breeding approaches. Beneficiaries will include wheat breeders globally, the public sector programmes in Ethiopia, Kenya and India, and small-holder farmers in developing countries, via more sustainable crop productions systems associated with genetically resistant varieties. These beneficiaries will gain from this research by several means, all of which are centred on more sustainable crop production practices.

The identification and functional profiling of resistance genes with broad spectrum recognition specificities will allow breeders to deploy strategic gene combinations in their new varieties. This will have important benefits for breeders who will be able to extend the life of desirable varieties as they should remain resistant over longer periods of time. The delivery of tightly linked genetic markers will also make this process more efficient and will enable them to build pre-breeding germplasm or parental lines with stacked gene combinations.

At the same time, this will benefit small scale farmers who will be able to adopt and grow varieties with less risk of crop failure due to the appearance of new Pst races. These broad-spectrum resistant varieties will also reduce fungicide applications while protecting yield. This will benefit farmers directly by reducing or even avoiding exposure to fungicides and will translate into increasing income by reducing production costs associated to these applications and protecting/increasing yields. In many cases, farmers cannot afford fungicides, so genetic resistance is the only viable option to avoid crop failure.

The national breeding and science programmes from all countries involved will benefit by the investment in infrastructure and capacity development activities which are included in this project. We strongly believe in the forging of mutually beneficial partnerships and that training the next-generation of crop scientist is a key element in establishing these links that will secure long term relations. This proposal brings together a unique combination of disciplines that will provide an exciting training ground for a cadre of excellent young scientists. The resulting innovation and training will provide the next generation of skilled crop scientist, with benefits beyond the immediate outcomes of this project.

In summary, the combination of these factors will help enhance food security, develop more sustainable agriculture practices, increase opportunities for small scale farmers to improve their income, and establish long-term working relationships between the different partners involved.


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Bevan MW (2013) Genomics reveals new landscapes for crop improvement. in Genome biology
Ramirez-Gonzalez RH (2015) PolyMarker: A fast polyploid primer design pipeline. in Bioinformatics (Oxford, England)
Description • We have sequenced gDNA of 52 PST isolates from Europe (34), East Africa (9), India (4), Pakistan (2) and China (3) at ~50x coverage.

• We have sequenced 9 time points (x3 reps) for an infection time course with UK PST isolate. We have used this data to re-annotate the gene models to make best use of the transcriptome data. The more in-depth analysis of this data is currently on-going.

• We have evaluated over 500 Watkins accessions for yellow, leaf and stem rust in East-Africa, India and UK. Based on the phenotypic evaluations we have chosen 39 accessions of high priority due to their strong resistance or due to the consistent moderate resistance across regions. These 39 accessions have been crossed to AvocetS to develop mapping populations to be screened within objective 4. A subset of the populations (5) will be available to screen as F2:3 families in 2014, whereas the rest are being developed by single seed descent into populations

• We conducted a 5-day "soft-skills" workshop in Njoro in late August 2014. The workshop was a great success as evaluated by the 15 participants. These included SCPRID PhD students, several Kenyan PhD and MSc students, and members of other SCPRID projects (PEARL awardee; SPCRID striga project).

• We are currently training 5 PhD students within the project.
Exploitation Route Not applicable at this moment
Sectors Agriculture, Food and Drink