There is a large and growing market for plant-based protein, within which the imperative for price competitiveness and sustainability continues to drive a major shift in preferred raw material from soybean and pea to faba bean. Prior UKRI funded research by the applicants has developed faba bean genome maps and uncovered sequence variation controlling a variety of simple and complex faba bean seed traits including, crucially to this application, levels of anti-nutrients as well as nutrients in the seed. The team has thus secured a world-leading position in understanding the genetic architecture of faba bean seed storage protein content and composition. They have already laid the foundations for commercial exploitation of this knowhow by conducting market research into the demand for faba bean varieties with enhanced protein content, quality or both (the 'Fabaplus' concept), by generating novel nutritionally enhanced breeding material and validating cutting edge methodologies for selection of commercially viable candidate varieties with uniquely high content and high quality of seed protein. However, the long duration of the breeding process and uncertainties over which characteristics other than seed nutritional density/quality might be decisive in determining the commercial success of a putative 'Fabaplus' variety mean that it is difficult for commercial bean breeders to invest in the concept as it currently stands. Therefore, it is appropriate to request UKRI support for a development plan which will take the 'Fabaplus' breeding pipeline to the point where novel candidate lines with both competitive yields and unique quality characteristics can be evaluated for their technical performance by commercial partners in their plant protein concentration processes. The programme essentially involves scaling up efficient DNA and protein profiling of 1,000s of individual lines from breeding populations, so that we can stack beneficial DNA variants and process a sufficiently large population to find rare individuals combining competitive commercial yield potential with unprecedented levels of high-quality protein. To assess the utility of 'Fabaplus' trait enhancements, we have partnered with a plant protein processor who has specifically targeted faba bean as a raw material fitting the sustainability and nutritional values required by their business models. Our processor partners will conduct side-by-side evaluations of 'Fabaplus' candidate varieties alongside best current commercially available raw materials to determine any gains in efficiency or end product quality attributable to the raw material, forming the basis for an assessment of economic returns that will drive demand for 'Fabaplus' varieties. Two alternative routes to commercialisation are envisaged: either a dedicated new spinout company will be formed to finish and submit 'Fabaplus' varieties for Plant Breeder's Rights or the further breeding and commercialisation will be pursued through partnership with commercial breeders under a licensing arrangement. An advisory board of commercial bean breeders and end user partners will provide ongoing feedback throughout the programme and a forum through which optimum commercialisation routes can be developed

Turnip yellows virus (TuYV) is a damaging pathogen severely reducing yields of oilseed rape (OSR) (3rd most widely grown crop in UK). UK losses are estimated at >15%, costing £69 million/annum. It also significantly reduces the yield (up to 65%) and quality of brassica vegetables (e.g. cabbage and sprouts). In earlier BBSRC-funded research, we identified sources of natural plant resistance to TuYV that were effective against the different strains of TuYV. The aim of the proposed research is to work together with commercial plant breeders from different companies to provide plant lines with our resistances to TuYV and tools (molecular markers) needed for our commercial partners to move the resistances in to commercial OSR and vegetable brassica crop varieties. The breeding of the virus-resistant varieties will increase yields, thereby helping food security and also reduce the amounts of pesticides farmers spray on crops, in attempts to stop the greenfly vectors spreading TuYV

Although oilseed rape (OSR; Brassica napus) has traditionally been grown as the most profitable break crop, a loss of controls for cabbage stem flea beetle (CSFB; Psylliodes chrysocephala), has resulted in UK cropping area declining by 35% between 2012 and 2019. The National Farmers Union (NFU) estimate the removal of neonicotinoid seed treatments has cost farmers ~£94 million/year in lost opportunity and crop loss. Additional costs have been absorbed by the UK crushing industry because of the need to import OSR. Collectively, this poses a serious risk to the viability of the UK OSR industry and current farm crop rotation practices. With the withdrawal of chemical controls, resistant cultivars are central to supporting Integrated Pest Management (IPM) strategies. However, unlike plant-pathogen interactions, our understanding of the interactions between host plants and chewing insects is limited. CSFBs are attracted to glucosinolates, chemicals used by Brassica species to deter non-specialist insect pests. Even if B. napus has defence or resistance mechanisms that deter CSFB feeding, the genetic control of such mechanisms and whether they can be exploited to breed for resistance has remained an open question. There are no known examples of resistance in B. napus and little knowledge of resistance mechanisms within our UK crop species. No resistant cultivars are currently available for any insect pest of OSR. This proposal builds on preliminary data using controlled feeding studies and field trials, which shows that variation for reduced adult CSFB feeding is present within a diverse panel of B. napus. The panel, comprising historical varieties of winter and spring OSR, Chinese OSR, swede and kale, contains genetic diversity which is unlikely to be present in elite cultivars. This has enabled us to identify loci associated with CSFB feeding damage. Controlled larval infestation studies within this population have also identified variation in the numbers of emerging adult CSFB, demonstrating the presence of resistance to CSFB larvae. Together these observations indicate that some varieties of B. napus carry genes which can 1) deter adult CSFB feeding and 2) confer resistance against larval infestation or reduce larval fecundity. If identified, this variation can be exploited to breed OSR resistant to both damaging stages of CSFB. This proposal developed by two research institutes (JIC and Rothamsted Research), seven major plant breeders and the OSR growers' Levy board (AHDB), aims to discover loci associated with adult CSFB feeding and larval resistance in B. napus. In parallel, we aim to develop an understanding of crop adaptations which affect OSR-CSFB interactions. This will be coupled with larval development studies, gene expression analysis and metabolite profiling to further elucidate key mechanisms by which Brassica plants identify and defend themselves against beetle attack. Key genes implicated in resistance and defence responses will be investigated using candidate gene studies in model plants, including candidate genes which underlie two loci implicated in the supporting data. Collectively, this knowledge, combined with germplasm and markers that will be used by participating breeders to integrate resistant alleles into commercial breeding pipelines, will facilitate the introduction of tolerant varieties into the UK OSR market.

Pulses, in particular peas and broad beans, are important crops both in the UK and worldwide and they are grown as extensive monocultures. Even with long rotations, the crops are vulnerable to major epidemics of economically important pests and diseases, of which downy mildews (caused by the oomycete biotrophic pathogens Peronospora viciae f. sp. pisi (Pvp) and P. viciae f. sp. fabae (Pvf) in peas and beans, respectively) are the most serious. Breeding companies are challenged to produce cultivars with new resistance genes and will benefit from access to crop wild relatives carrying new resistance genes. The disease is managed through deployment of resistant varieties and chemical controls; however a lack of information on prevalent isolates can lead to serious yield losses in crops grown on contaminated sites through uninformed variety selection. Although a differential set of plant cultivars is available to identify the virulence genes in pathotypes of Pvp/Pvf, the test is too time-consuming to be of immediate use to commercial growers and does not allow rapid monitoring of the prevailing isolates. In addition, generating a model for pathogen spread is impossible using current methods. The problem is exacerbated by reports of resistance of oomycete pathogens to pesticides such as metelaxhyl. Without adequate control regimes, pea and broad bean production will incur greater crop wastage and it is therefore imperative that methods are developed to decrease growers' reliance on pesticides for the control of downy mildew. Deployment of pulse cultivars resistant to prevailing isolates is the most promising approach. Use of appropriate molecular tools will enable breeders, epidemiologists, modellers and growers to: a) identify the prevailing virulent isolate; b) investigate the epidemics of disease; c) monitor pathogen movement and d) deploy the appropriate cultivar(s) resistant to the prevailing isolate rapidly and thus control the disease in an environmentally friendly and sustainable manner. Accurate advice to growers about resistant cultivars requires correct information on the virulence of Pvp/Pvf races within the locality. However, diagnosing the pathogen at the isolate level requires the right tools. The innovative approach described in this project focuses on the development of molecular tools for accurate identification of Pvp/Pvf isolates as well as for breeding for resistance. We aim to identify new resistance sources to include in breeding programmes and develop molecular markers to enable rapid identification and monitoring of pathogen isolates. We will use next generation sequencing to identify polymorphisms in several isolates. These polymorphisms will then be utilised to generate isolate-specific markers. Once identified, markers will be tested under laboratory conditions and subsequently will also be checked in commercial fields. In addition, we will use biological control agents to control downy mildew disease. These will lead to increased crop productivity, reduced reliance on pesticides and less wastage from diseased plants.

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.