The central objective of this proposal is to apply state of the art high throughput breeding and phenotyping approaches to the genetic improvement of oats, focusing on yield, and grain and milling quality, key targets for the economic sustainability of the crop and for the milling industry. The project addresses some of the major challenges facing UK agriculture in terms of the sustainable production of safe and nutritous food. The overall aim of this LINK project is to incorporate high throughput approaches to the IBERS oat breeding programme, to develop strategies to improve yield and other targets ranked as priorities by our industrial partners which are currently difficult or impossible to select for at early stages of breeding cycles. Marker assisted selection (MAS) represents one route to achieve this. It has been successful for introgression of major traits controlled by one or a few genes of large effect, but is difficult with more complex traits governed by many genes, each with a small effect. MAS is used in the IBERS oat breeding programme, largely based on predictions derived from a few markers linked to large effect quantitative trait loci (QTL). Association mapping (AM) will be used to identify further marker-trait associations enabling rapid selection or introgression within the breeding programme. In this project, genomic selection (GS) will be applied to a range of traits, and selections will be validated by comparison with breeder and conventional marker assisted (MAS) selections. Increasingly complex models will be developed in the course of the programme, and an accelerated breeding cycle driven by GS and MAS will be initiated. Traits which may predict yield will be identified by detailed phenomic and field trial analysis of a model winter oat population and an association genetics panel of advanced breeding lines. Metabolic profiling and micro-scale analytical methods will be used to develop further predictive screens. Chip-based high throughput genotyping will be used to predict breeding values; genotype and phenotype data will be incorporated into a pedigree database to further facilitate 'intelligent' breeding design. The existing Illumina 6K iSelect bead assay will be expanded to include SNPs identified from UK winter and European germplasm which have significantly different genetic bases from the bulk of varieties used to develop the initial assay set. Genotyping by Sequencing will become the main platform by the end of the project to take advantage of expected sequence throughput improvements. This project proposal addresses sustainable agricultural production at the interface of two BBSRC strategic priority areas: crop science and healthy and safe food. It is of high strategic relevance, specifically in enhancing crop productivity and quality, enhanced nutritional composition, increasing sustainability of crop production and understanding and exploiting genomics and the genetic diversity in plants (crop science). It will also investigate the potential of novel nutrient supplies from plants (healthy and safe food). This proposal is being submitted through the BBSRC stand-alone LINK scheme. The project will benefit from the involvement of the major oat variety development company in the UK (Senova) and the British Oat and Barley Millers Association (BOBMA) representing the major oat milling companies within the UK such as PepsiCo/Quaker, Morning Foods, European Oat Millers, Grampian Oats, Hogarths and SpeediCook. Involvement of industrial partners will allow for identification and review of key targets and delivery of the outcomes of this project alongside the academic partners.

Higher agricultural productivity and sustainability is critical to meeting the global challenges of food security in the presence of climate change. Legume crops are a critical source of plant-based proteins for people and animals. As the world demand for animal products increases, the demand for vegetable proteins as animal feedstocks also rises and the UK in common with other countries faces a shortfall in domestic vegetable protein production capability. In the EU 70% of the protein fed to animals is imported, mostly soyabean or soya meal with soya meal accounting for 33% of the protein in UK livestock feeds. In 2011-12 UK imports of soya products reached 1.83 million tonnes, the majority of this being transgenic soya imported from South America. Increasing the amount of UK grown protein to replace imported soya products is recognised as a major challenge for the UK animal feed sector. In this LINK proposal we will develop and apply new genetic approaches to enhance the nutritional value (protein and water soluble carbohydrate) of the pea (Pisum sativum L.) seed, to increase the use of pea as a high quality feed in animal diets, reducing the UK protein deficit from the import of soya products and also delivering environmental benefits to livestock production systems. The proposal builds on knowledge gained in BBSRC, EU, Defra, Innovate UK and levy board-funded research on the genetics and agronomy of pulses that have led to the development of novel lines of pea with higher protein content. We will use our expertise in plant genomics, pea genetics and breeding, agronomy, plant chemistry and animal nutrition to integrate the germplasm with improved grain composition into improved pea varieties. With industry partners from the poultry and pig sector as well as crop developers, we will analyse the impact of replacing soya with these new pea varieties in feed rations on the growth of monogastrics and poultry and the economic and environmental impact of their inclusion. Although the focus is on poultry and monogastrics, the project will provide information on the value of including these new pea lines for other sectors (ruminants and aquaculture).

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.