New Investigator Award: Rapid identification of genes and pathways that increase resistance to yellow rust disease of wheat

Rust is one of the most devastating diseases of wheat, causing severe yield losses in the UK and globally. Wheat, similar to all plants, has a sophisticated immune system that is currently under-deployed in agriculture. The aim of this project is to improve cultivated wheat by isolating novel sources of rust disease resistance and making them rapidly available to wheat breeding programs. Wheat is the most prevailing plant on earth as wheat crops occupy nearly 25% of world agricultural land. With annual production at more than 650 million tons globally, wheat provides a quarter of all calories and fifth of protein supply to humanity, and yet the annual yield increases are critically below the rate required to feed the growing human population. According to the predictions from the World Bank, agricultural productivity will need to increase as much as 70% to feed 9 billion people by 2050. Growing wheat varieties resistant to diseases is an economical and environmentally friendly solution to increase yield on available agricultural land while reducing growth costs.

As a New Investigator, I am establishing a research programme focused on improving resistance of wheat to a broad range of fungal diseases. I am leveraging recent technological advances, such as cutting-age sequence technologies, for the efficient study of highly complex wheat genome. I plan to rapidly identify novel rust resistance genes derived from cultivated wheat and make these genes accessible to traditional non-transgenic breeding programmes. I have already carried out a screen for new yellow rust resistant mutants of wheat that I believe are novel and can be a new source of disease resistance. By testing resistance in our wheat lines against a variety of wheat pathogens, including mildews and Septoria leaf spot, my group will identify sources of broad-spectrum resistance. By applying new sequencing technologies in a highly efficient manner we will dramatically reduce the time of wheat gene isolation from 15-20 years to just 2-3 years. Furthermore, I am aiming to investigate the mechanisms of plant resistance and to study the evolution of these mechanisms and their diversity in wheat. Isolation of novel rust resistance genes that are derived from cultivated wheat will make these economically important traits immediately available for ongoing wheat breading programs. As our sources of resistance are derived from elite cultivars, such introduction can be achieved with conventional non-transgenic manner. Knowing the genomic locations of new disease resistance is key to accelerate this process. The gene isolation approach developed here will be applicable to any trait of interest.

The major output of my proposed project will be new disease resistance genes and the new tools that plant breeders can use to introduce resistance into the most commonly grown, high yielding wheat varieties. I foresee a great benefit from this project not only to wheat breeders and wheat growers, but also to society in general. Advanced understanding of plant defense systems and deploying it to control plant diseases is a timely economical solution to increase food supply and reduce use of pesticides.

In this project I aim to isolate wheat genes responsible for gain-of-resistance to yellow rust disease in the mutant population of elite tetraploid wheat cultivar, Kronos. At The Sainsbury Laboratory, we will test our previously identified mutant lines for broad-spectrum resistance to wheat pathogens (powdery mildew, Septoria and wheat blast). We will examine the stage at which pathogen is stopped by microscopy and pre-priming of defence responses by q-PCR. Leveraging the recent advances in wheat genomics at The Genome Analysis Centre, we will establish a rapid approach for mapping wheat genes by exome capture and sequencing reducing the complexity of wheat genome (17 Gb). We will sequence the gene space of the F2 populations of resistant mutants using exome-capture design (86 Mb) and identify mutations linked to resistance with our mutation calling pipelines, providing large amount of marker data. For high-resolution mapping we will design small exome-capture to completely cover the identified chromosomal interval and sequence the region with PACBio technology. We will study natural and induced diversity in the target loci in wheat TILLING populations and 1,000 wheat cultivar and related species with published yellow rust resistance Genome Wide Association data. Specifically, I propose to:

- Adopt semi-automated assays for quantifying rust growth inside wheat leaves.
- Test mutant wheat lines for pre-priming of defence response pathways.
- Evaluate selected mutants for the broad-spectrum resistance to multiple pathogens.
- Introduce new sources of resistance to the elite UK and European wheat varieties.
- Identify markers linked to resistance using wheat exome-capture and mapping-by-sequencing approaches.
- Clone and validate gene(s) responsible for broad-spectrum resistance to yellow rust.
- Identify natural and induced diversity in the resistance loci.

This New Investigator proposal directly addresses BBSRC's key strategic priority: "Sustainably Enhancing Agricultural Production" by providing new sources of disease resistance to yellow rust that can lower dependence on fungicides. Our approaches are underpinned by promotion of 'new ways of working' to accelerate wheat improvement.

According to the UN Food and Agriculture Organization, 30% of global wheat production is at risk due to wheat rust diseases (1). In the UK, wheat rust epidemic is exemplified by the 'Warrior' race that emerged in 2011 and pushed yellow rust to be the top threat to wheat production (2). Although effective against rust diseases, fungicides are often harmful to human health and/or environment. The cost associated with repeated application of fungicides greatly reduces farmers' profits. In developing countries, fungicides are often not affordable. In 2009 due to the harmful effects on human health, the European Parliament voted to tighten rules on pesticide use and ban 22 chemicals (3). By 2020, the EU plans to ban another 40 chemicals to reduce environmental damage. The Anderson Centre report, commissioned by the Agricultural Industries Confederation, the Crop Protection Association and the National Farmers' Union, estimated that if the pesticide control of wheat diseases was unavailable today, farmers' income would drop from £1.9 to £1.5 bn a year - 21% income loss (4). Disease control with resistant wheat varieties lowers the dependence on fungicides, and provides direct benefit to human health and sustainability of agriculture. New sources of disease resistance in wheat are urgently needed as current varieties could fall behind against newly emerging pathogen strains. These discoveries will need to be rapidly introduced to local wheat varieties to minimise crop losses.

The proposed work will provide new sources of resistance to combat yellow rust that can be deployed today in a conventional non-transgenic manner and lowering dependence on pesticides with a potential 10-20% savings to the farmers. We will also provide the tools for rapid integration of our findings into the current breeding programmes, building capacity to rapidly map, clone and breed disease resistance genes using the newest wheat genomic information. Beneficiaries include wheat breeders, wheat growers and wheat consumers. Wheat breeders and growers will benefit from the genetic material and markers we will produce as it will help them to incorporate new disease resistance loci into high yielding wheat varieties. The genetic material with improved disease resistance will be available from the beginning of this project, and the markers within the first two years. Wheat breeders will benefit immediately from our methodologies for efficient use of the wheat genomic resources in trait improvement. As our methods are generally applicable to accelerating discovery of wheat traits from forward genetic screens, they can be applied to general wheat improvement, including abiotic stress tolerance and yield improvement. Wheat breeders and researchers alike will greatly benefit from adopting these strategies. The researchers appointed on this project will benefit from cross-disciplinary training and having an outstanding opportunity to observe the translational power of their discoveries. They will have opportunities to interact with world-class researchers as well as industry, which will put them in a unique position to advance their future careers in either the public or private sector.

References: (1) FAO Wheat Rust Disease Global Programme WHEAT RUSTS - Constant threat to wheat crops around the globe, 2014 (2) AHDB Cereals and Oilseeds. Increasingly diverse UK cereal rust populations need close monitoring, 2015. (3) B. Ilbery, D. Maye, J. Ingram, R. Little, Geoforum 50, 129-137, 2013. (4) The effect of the loss of plant protection products on UK agriculture and horticulture and wider economy. The Andersons Centre, 2014.