Developing new strategies to manipulate yield and pest and disease resistance by marker-assisted selection (MAS) underpins the UK's strategy to generate improved wheat varieties. Academic laboratories, genotyping service providers and breeding companies use MAS to track the inheritance of a host of loci controlling desirable traits such as disease resistance, drought tolerance and yield. Until recently most laboratories have used microsatellite markers in their MAS projects, while these markers continue to be used, for many species Single Nucleotide Polymorphisms (SNPs) have become the marker of choice due to their ease of use and scoring and their ability to be automated with relative ease. However, in allohexaploid wheat the task of identifying similar useful sequence polymorphisms is problematical due to the occurrence of homoeologs from the A, B and D genomes. In this proposal, in collaboration, the John Innes Centre, IDna Genetics and KBioscience and Bristol University will develop both a wheat SNP database and a flexible genotyping platform for wheat. The utility of both will be validated by applying the tools and technologies to several exemplar projects. If successful users will be able to access the technology via two routes: The first consists of an in-house set-up requiring only basic molecular biology equipment (PCR machine and fluorescence plate reader). In this case, users would use the database to help them decide which assays to run and which primers/reagents (all publicly available through the database) to order and suggestions as to where these might be obtained. This constitutes a very low barrier for adoption as most users will be able to perform these SNP assays in house at the scale that best fits their purpose. This level of platform will be employed for the work carried out at JIC. The KASPar platform will replace JICs existing SSR genotyping service and, like the existing service, will be available for external work. An aliquot of the full set of KASPar primers will be kept at JIC and made available via this service. The second form of access consists of outsourcing to competitive service providers, such as KBioscience and IDna Genetics. Both companies have high-throughput platforms installed which will help lower costs and both will be set up to run all the KASPar assays developed in this project. The user would only need to provide genomic DNA and a list of which assays to run. In addition to KASPar, members of the community will be able to use the database to access a range of alternative genotyping technologies such as Illumina GoldernGate/Infinium/SureSelect, etc. For instance, the database will enable researcher to either design suitable probes for ordering from the appropriate technology supplier or they will be provided with details as to who offers the required technology on a commercial bases. This database will then be updated until at least 2017.

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).