Diseases of crops present major threats to the security of food supplies throughout the world. In the UK, our more important crop, wheat, is challenged by several significant harmful organisms including fungi, viruses and insects. Food production which is environmentally and economically sustainable requires crop yields to be maintained despite attacks by these pathogens. The two main pillars of disease control in arable crops are pesticide applications and the cultivation of resistant varieties. New legislation by the European Union will prevent increasingly severe obstacles to the introduction and use of pesticides from 2014 onwards, especially after 2018. Improved disease resistance is an important objective for wheat breeding but will become even more crucial to project food production in the UK once the new EU regulations come fully into effect. Almost all research on plant diseases, whether of crops or model species, focuses on single diseases. In field conditions, however, it is normal for crops to be attacked by epidemics of several pests and parasites simultaneously. This proposal takes a novel approach to researching the genetics of resistances to multiple diseases and their impact on yield. A particularly important goal is to identify genes for resistance to one disease which neither reduce yield nor increase susceptibility to other, non-target diseases. We will achieve this aim using association genetics, an approach which has proved extremely powerful in research on the genetics of disease and other traits in human populations. We will study a panel of 480 wheat varieties, including varieties which are commercially significant at present and their progenitors. We have chosen to study the four main diseases caused by fungi that attack the leaves of wheat plants. Together, these diseases present the main actual and potential threats to yield of wheat in UK conditions. There is currently good resistance in UK wheat varieties to powdery mildew and it is important that this desirable situation continues. Resistance to Septoria tritici has improved over the last ten years but this is still the most important wheat disease. Resistance to yellow rust is generally good by international standards but is often not durable, being quickly overcome through evolution of virulence in the fungus. There have been severe epidemics of brown rust in the UK in recent years and it is important that the average level of resistance of our wheat varieties to this disease is improved. An important goal is to generate a resource for use by the whole wheat research community. The association genetics analysis and the associated data, seed and DNA stocks will be a excellent resource for research on traits which are currently important. It will also, however, enable breeders and geneticists to respond to new threats, such as diseases which become important rapidly as a result of climate change or new agronomic practices; this has happened recently with Ramularia leaf spot of barley in northern Europe, including the UK. In summary, the association genetics approach will enhace current wheat breeding, especially for disease resistance, and enable us to be forearmed against future challenges.

Wheat is the UK's major food crop. A major constraint on wheat production is the disease yellow rust (YR), caused by the fungus Puccinia striiformis f.sp. tritici (Pst), with yield losses up to 50% in untreated crops. The two major control measures for this disease, used in combination, are use of resistant varieties and application of fungicides. Fungicide application is effective but expensive, limited by weather conditions and increasingly restricted in use due to environmental concerns. Host (i.e. wheat) resistance can also be very effective, with several known resistance genes conferring immunity to known races of Pst. However, populations of the pathogen regularly change and resistance genes suddenly become ineffective when the pathogen mutates. In Europe, there was a recent rapid incursion of an exotic Pst population, which is much more diverse than the established population it has displaced. As a result, there have been dramatic and ongoing changes in the patterns of YR resistance in commercial wheat varieties. In 2016 alone, seven varieties on the UK wheat Recommended List had their resistance ratings substantially reduced, with significant cost impact on growers. Breeding improved wheat varieties with effective, long-lasting YR resistance to withstand current and future incursions is now a top priority for northern European (NE) wheat breeders. In Yellowhammer, we will employ a strategy based on detecting and utilizing multiple race non-specific adult plant resistance (APR) genes, for long-term genetic control of the disease. These genes usually confer partial resistance, are characterized by reduced and slower pathogen growth, and can be 'stacked' with each other or with 'major" genes in the same plant to provide effective long-lasting resistance. We previously identified several APR genes - but finding the most effective combinations is challenging as different genes interact with each other in complex ways. To address this challenge, we are collaborating with seven NE breeding companies and the UK's Agriculture and Horticulture Development Board to develop experimental wheat populations based on elite European varieties, but which differ in the combinations of YR APR genes they carry. We will use these to: 1. Identify the most effective combinations of APR genes, and the times of the season they become effective, in field tests at twelve sites in NE over four years. We will investigate what is the most effective combination of strong and weak APR genes to achieve YR resistance in wheat. We will also determine the effectiveness of APR genes in hybrid wheat and any side-effects APR genes have on grain yield. 2. Determine, using 'microphenotyping', the timing and location of action in the plant of different APR genes involved in the pathogen-host interaction, helping us select functionally complementary APR genes to combine. 3. Identify which wheat genes and genetic pathways are switched on or off in response to the pathogen in the presence of different APR gene combinations in order to understand how to best assemble APR gene combinations with complementary molecular genetic mechanisms of resistance. We will also conduct field pathology trials of newly available populations and varieties to identify new APR genes. The results will allow us to determine the best combinations of resistance alleles to stack, and provide new genetic markers to aid the process. Results will be validated in active commercial breeding material and will immediately be translatable into the breeding programs of our commercial partners, enabling them to breed more durably resistant wheat varieties equipped to resist the current Pst population and potential future incursions. This will improve UK arable production and food security, and reduce environmental harm, as farmers benefit from having access to more consistently performing, longer-lasting varieties with reduced fungicide requirements.