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.

Fusarium head blight (FHB) of cereals is caused by a number of fungi, chiefly Fusarium species. It is of particular concern because the Fusarium species produce trichothecene mycotoxins (DON, NIV, T2 and HT-2) within grain that are harmful to human and animal consumers. FHB disease poses an increasing threat to the UK wheat and barley crops. New species have appeared and spread in the UK for which climate change may, in part, be responsible. Future predicted climate changes are likely to exacerbate risks of epidemics in the UK. The EU recently set limits for DON and limits for T2/HT-2 are imminent. It is vital that the UK is positioned to be able to comply with this legislation. It is widely recognised that resistant varieties offer the best option to control FHB. All wheat and barley breeders consider it as a major but difficult target for resistance breeding. Incorporation of high levels of resistance to FHB into wheat and barley will be critical to prevent DON, T2, HT-2 and NIV mycotoxin contamination of grain from becoming a major problem for all elements of the UK food and feed chains. Timely application with appropriate fungicides can restrict disease development and mycotoxin accumulation. Under moderate to high disease pressure, however, fungicide application often fails to reduce DON contamination to below EU legislative limits in susceptible varieties such as those currently grown in the UK. Our previous work showed that much of the susceptibility of UK varieties is due to linkage between a gene that affects the height of wheat, Rht2 (also referred to as Rht-D1b) which is in almost all UK varieties, with a gene nearby on the chromosome that increases susceptibility to FHB. This association must be broken to enable breeders to produce FHB resistant varieties with acceptable agronomic characters. The project will produce molecular markers to the region about Rht2 allowing plant breeders to maintain this agronomically important gene in their breeding programmes while selecting against the linked FHB susceptibility factor. This project aims to identify resistance to Fusarium head blight (FHB) in wheat and barley that will function against all the causal fungi associated with this disease. This project will focus on the identification of Type 1 resistance (resistance to initial infection) in wheat and barley. We have developed new tools to characterise so-called 'Type 1' resistance (resistance to initial infection), which is important for preventing infection of wheat and barley against Fusarium species that produce DON mycotoxin and those that produce the more toxic T2 and HT-2 toxins as well as against non toxin producing FHB pathogens such as Microdochium species. Plant breeding companies can immediately use the plant materials, genetic knowledge and molecular markers linked to FHB resistance within their breeding programmes to produce new resistant varieties with good characters for growing as crops in the UK. This project will determine how fungicide application influences disease and toxin accumulation in varieties with different levels of FHB resistance. The project will demonstrate how individual FHB resistances affect the RL disease score, revealing how many, and what forms of resistance are required to ensure that toxin levels in UK grain do not exceed EU limits. The project will identify the components required to establish a sustainable, integrated approach to ensure that toxin levels in cereal grain remain below EU limits. An integrated approach, based on varieties with significantly enhanced resistance and appropriate fungicide application offers the best means to achieve sustainable control of FHB and minimise the risk of mycotoxins entering the food and feed chains.

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.

Currently Europe produces only about 30% of the plant protein needed for supplementary protein in feed, resulting in import of 40 million tonnes of soya bean and soya meal per year (Watson et al. 2017). This imbalance in the European agricultural system is due to the lack of an economically competitive grain legume protein crop that can match cereals for farmer profits. The current system dominated by cereals is not sustainable since it enforces vast protein imports and requires large supplements of energy-expensive mineral fertilizers, since cereals, unlike legumes, are not able to fix nitrogen. The ProFaba project aims to boost protein production in Europe by improving faba bean (Vicia faba) as a European protein crop, thereby markedly contributing to a more balanced and protein-self-sufficient agricultural system. There is currently a growing interest in faba bean, and several national projects have been launched to drive the much-needed acceleration of faba breeding, including NORFAB, Papugeno, BEANS4N.AFRICA, PeaMUST, and Abo-Vici. At recent international meetings, researchers from all of these programs discussed current activities and identified complementary areas of expertise as well as common goals. As a result, the ProFaba ERA-NET project will bring partners together with complementary expertise in genomics, bioinformatics, quantitative genetics, insect resistance, disease resistance, abiotic stress tolerance, nitrogen fixation, field phenotyping, breeding, and climate and phenological modeling to tackle the main obstacles to faba bean success as a protein crop. Taking a collaborative approach focusing on common resources, ProFaba will build a common reference and data repository for faba genome, genotype, and phenotype data, ensuring easy communication throughout the faba community. ProFaba will leverage these resources by developing common diversity panels and breeding lines, which will be phenotyped for agronomic traits in five different locations from the South to the North of Europe. This will allow deciphering the genomic architecture of faba traits, understanding genotype by environment interactions, and direct incorporation of this knowledge into active, predictive breeding programs through the participating breeders from Denmark, Germany, France and Spain. ProFaba project results will additionally be disseminated through breeder and grower conventions to the wider group of stakeholders as well as through scientific publications and conferences. ProFaba will focus on the most critical faba traits across Europe, and phenological and climate change models will be used to understand and predict future breeding targets for specific regions. ProFaba will work with both spring- and autumn-sown material to understand genetic differences and improve frost tolerance of autumn-sown germplasm, which could lead to rapid changes in management practices and increased yield in colder climates. Low soil pH restricts the growth of faba bean in wet climates, and ProFaba will establish the genetics and physiology underlying faba acid-soil tolerance to enable its manipulation in practical breeding. To drive reduction in pesticide use, and thus promote faba bean ecosystem services for pollinators, ProFaba will perform multi-location testing of bruchid-resistant germplasm and map the alleles associated with resistance. As an additional strategy to ameliorate the effects of pollinator decline, ProFaba will dissect and understand autofertility, which allows persistent high yield in the absence of cross-pollination. In terms of resource use efficiency, biological nitrogen fixation through symbiotic interactions with rhizobia is a critical but poorly understood trait. ProFaba will address this by identifying faba bean germplasm, which effectively selects for efficient nitrogen fixing rhizobia, and by taking the first steps in establishing efficient nitrogen fixation as a breeding target.

Ramularia leaf spot, caused by the fungus Ramularia collo-cygni, has spread rapidly to become a major disease of barley in Britain and many other parts of Europe. It was first recognised in the UK in 1998 and is now important in Scotland, especially on spring barley, and is spreading into winter barley in England. The rapid, recent increase in its importance means it is poorly understood in terms of scientific understanding of the disease and the pathogen, methods of crop disease management are currently limited to fungicide applications and breeding of barley varieties for resistance to Ramularia is in its infancy. There is thus both a pressing need to understand the disease and an exciting opportunity for research to combat it. This LINK project will take an integrated approach to developing methods to controlling Ramularia which will remain robust despite rapid changes in the environment and farming systems. This will help to support production of barley, the UK's second most important crop, in a way which is economically and environmentally sustainable despite an increasingly variable climate. For control of Ramularia in the short term (up to 5 years), we will develop a forecasting system to increase the precision of fungicide applications and thus to minimise the volume of active ingredients applied to barley crops to control Ramularia. For the medium term (up to 10 years), our research will aim to break the chain of transmission of the disease by reducing contamination of barley seed stocks, partly through improved methods of identifying contamination and partly by improvements in seed treatments. For the longer term, our research will support the efforts of barley breeders to select barley varieties which are suitable for UK markets and are not susceptible to Ramularia. We will do this partly by research on the genetics of resistance, by identifying varieties which have different genes for Ramularia resistance and can thus be crossed to produce barley lines with better resistance than their parents, and partly by improving methods of selecting barley varieties with resistance to Ramularia. This research will be underpinned by advances in knowledge of the biology of the disease, unravelling the complex interactions between physical stress, toxins produced by the fungus and the resistance of barley varieties to the fungus. Advances made by this project will give barley growers the ability to control Ramularia using well-timed applications of effective fungicides, the seed trade the opportunity to reduce the spread of the disease by minimising fungal contamination of barley seed and plant breeders the opportunity of producing barley varieties with resistance to Ramularia.