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Norwich, United Kingdom

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 439.75K | Year: 2016

Rust is one of the most devastating diseases of wheat, causing severe yield losses in the UK and globally. Wheat, similar to all plants, has a sophisticated immune system that is currently under-deployed in agriculture. The aim of this project is to improve cultivated wheat by isolating novel sources of rust disease resistance and making them rapidly available to wheat breeding programs. Wheat is the most prevailing plant on earth as wheat crops occupy nearly 25% of world agricultural land. With annual production at more than 650 million tons globally, wheat provides a quarter of all calories and fifth of protein supply to humanity, and yet the annual yield increases are critically below the rate required to feed the growing human population. According to the predictions from the World Bank, agricultural productivity will need to increase as much as 70% to feed 9 billion people by 2050. Growing wheat varieties resistant to diseases is an economical and environmentally friendly solution to increase yield on available agricultural land while reducing growth costs. As a New Investigator, I am establishing a research programme focused on improving resistance of wheat to a broad range of fungal diseases. I am leveraging recent technological advances, such as cutting-age sequence technologies, for the efficient study of highly complex wheat genome. I plan to rapidly identify novel rust resistance genes derived from cultivated wheat and make these genes accessible to traditional non-transgenic breeding programmes. I have already carried out a screen for new yellow rust resistant mutants of wheat that I believe are novel and can be a new source of disease resistance. By testing resistance in our wheat lines against a variety of wheat pathogens, including mildews and Septoria leaf spot, my group will identify sources of broad-spectrum resistance. By applying new sequencing technologies in a highly efficient manner we will dramatically reduce the time of wheat gene isolation from 15-20 years to just 2-3 years. Furthermore, I am aiming to investigate the mechanisms of plant resistance and to study the evolution of these mechanisms and their diversity in wheat. Isolation of novel rust resistance genes that are derived from cultivated wheat will make these economically important traits immediately available for ongoing wheat breading programs. As our sources of resistance are derived from elite cultivars, such introduction can be achieved with conventional non-transgenic manner. Knowing the genomic locations of new disease resistance is key to accelerate this process. The gene isolation approach developed here will be applicable to any trait of interest. The major output of my proposed project will be new disease resistance genes and the new tools that plant breeders can use to introduce resistance into the most commonly grown, high yielding wheat varieties. I foresee a great benefit from this project not only to wheat breeders and wheat growers, but also to society in general. Advanced understanding of plant defense systems and deploying it to control plant diseases is a timely economical solution to increase food supply and reduce use of pesticides.

Agency: GTR | Branch: BBSRC | Program: | Phase: Intramural | Award Amount: 105.33K | Year: 2015

Wheat yellow rust caused by the fungus Puccinia striiformis f. sp tritici is a substantial threat to wheat production worldwide and recently re-emerged as a major constraint on UK agriculture. Its importance to global food security is reflected by the significant contribution of wheat to the calorific and protein intake of human kind (approximately 20%). The devastating impact of this disease gives a deep sense of urgency to breeders, farmers and end users to improve surveillance. The overall aim of this project is to apply our recently developed “field pathogenomics” genomics-based pathogen surveillance technique to the surveillance of yellow rust, and undertake comprehensive global population genetic analyses of this important plant pathogen. The proposed research aims to: (1) Analyze the threat of potential exotic incursions of wheat yellow rust to the UK by mapping the global population structure, (2) exploit rust pathogen genotype data to confirm outbreaks on particular wheat varieties and look for associations between pathogen genotypes and host pedigrees, (3) generate information on whether genotypic diversity shifts over time at a locality and whether early appearing rust genotypes are predictive of late season genotypes and (4) develop appropriate open-source tools to ensure all data generated herein is released into the public domain as soon as possible and in a format that is suitable for breeders, pathologists and the wider demographic. This project aims to equip the UK with the latest genomic tools, facilitate more efficient varietal development by breeders, and help reduce the environmental and economic costs associated with fungicide applications, all of which will have a positive impact on the overall competitiveness and sustainability of the UK arable industry.

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 590.56K | Year: 2014

We live in a digital age where we increasingly rely on interconnected resources in our daily lives. Biological science, due to the very nature of the complexity of worldwide research avenues, is typically fragmented. Even though scientific information is published in peer-reviewed articles, it is often badly described and, until very recently, often unavailable to the general public because of journal licensing issues and expensive subscription costs. The field of bioinformatics (the analysis and management of biological data using computational methods) produces many freely available tools for data analysis and exposure that are incredibly useful to researchers. However, these tools often do not interoperate well, meaning that great effort is spent attempting to convert or tweak datasets to fit with other tools that further bioinformatics processes, hindering timely accurate reusable research. Couple this with the lack of descriptive information noted earlier, and knowledge that can be vital to one researcher, team or community can become at least unreproducible (thus letting others confirm findings) at worst unusable. Life scientists are people focused on investigating biological processes. This requires a lot of time, effort and fastidiousness in experimental observation, data collection and analysis. Typically for life scientists, more time is spent on the former: defining and publishing experimental methods and results. The latter, i.e. the data behind these results, is usually badly defined and largely unpublished. For computer scientists, the story is reversed - the focus is on getting to the data. This platform will bridge the gap between these two groups by providing tools and training to both life and computer scientists in the plant bioscience field, in order to help them get their data into the right formats and described uniformly for open research. To do this, the management, interoperability and curation of scientific datasets is key. Researchers need clear guidance and help to: - Manage their data in a concise relevant way that allows immediate reuse by others: Generating data is only one part of the picture. To back up scientific findings, data needs to be made available to others to allow the same degree of rigour and peer review that is enforced for published material. This is not an easy task because the tools and resources required to describe data well and to make data available are typically designed for the computer scientist. - Let them analyse their data easily: Large software development projects like Galaxy provide access to complex analytical tools - we are not aiming to reinvent the wheel in this regard. We aim to engage and collaborate with these existing providers to develop and exploit interfaces to these specialised software projects, so to let descriptive tools and analytical tools communicate efficiently. This project will address these issues directly, providing tools for storing, annotating and sharing valuable information as well as promoting clear guidance, training. Overall this promises to be a major boost to UK plant sciences research. This project aims to promote and build links between scientific knowledge and the tools used to generate that knowledge, addressing the lack of descriptive information about underlying data. By doing so, we will provide a platform comprising both existing tools and novel interoperability processes, allowing researchers easy access to methods of describing their work, feeding directly into analytical software, thus promoting clear and robust best practices in science. Open science is vital to the future generation of researcher, especially to realise the goals of transparent knowledge sharing. This project will remove the barriers that restrict researchers in making their findings freely available to everyone in a consolidated seamless easy-to-use fashion.

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 400.19K | Year: 2016

This proposal assembles a multinational academic and industry partnership to generate a reference octoploid genome sequence using a set of innovative experimental and computational approaches. This team includes industry and academic partners from the UK, Netherlands, Spain, Italy and Norway. Recent advances in strawberry genotyping technologies, for example the development of the Axiom IStraw90k SNP genotyping platform through the US-led Rosbreed programme (only possible due to the earlier part-BBSRC funded sequencing of the diploid strawberry genome) have led to the creation of multiple linkage maps, which highly saturate some areas of the genetic map for octoploid strawberry. However, the shortfalls of having only one of four of the diploid ancestral subgenomes sequenced is now apparent, as coverage of the non-vesca- like subgenomes is comparatively poor. Using some of the latest advances in bioinformatics and sequencing, combined with a technique termed massively parallel BAC sequencing, the proposed project team will first assemble a haploidised version of the octoploid strawberry genome. This will then be separated into separate parental genomes using a sequencing approach, which will combine using information from BAC sequences with single molecule optical mapping. Further anchoring of scaffolds will be deployed to assemble the genome into whole chromosomes. This approach has never been tried before and has only become possible in the last six months due to a number of recent innovations in genome sequencing and visualisation and is at the cutting edge of genome technology. This will resolve the genome into two haplotypes, one from each parent of the sequenced cultivar allowing inheritance to be tracked, which is an important innovation. Strawberry production is one of UK horticultures greatest success stories and domestic output still continues to expand, leading to over 80% self sufficiency when in season. The value of the crop to the UK recently exceeded £500m per annum, making it the highest value fruit crop in the UK. Globally, the primary problems of production remain the threats of oomycete and fungal diseases, which are now being addressed in the UK through a comprehensive research programme funded by both the UK industry, BBSRC and Innovate UK. The industry are supporting this proposal through the IPA scheme, as they recognize the need for an octoploid genome sequence, for marker assisted breeding (MAB) and other breeding techniques. MAB is a technique that uses the approximate location of important genes to improve the efficiency of selection in breeding programmes, actively deployed in a number of strawberry breeding programmes around the world, both in the public and private sector. However, due to the lack of an octoploid strawberry genome, progress at identifying the causative genes underpinning important disease resistance and fruit quality traits is slow. Identification and characterisation of gene function is important, not only to enable use of the latest generation of tools in cisgenic and targeted mutagenesis approaches in research and breeding, but also facilitates the study of questions of fundamental scientific interest about trait evolution in polyploids, which is of great important to both crop scientists and fundamental researchers. Further research on the evolution and structure of the genome and gene ohnologs will be of broad scientific interest. The impact of this research will be large, as the open and collaborative approach that is being taken in this project engages both industry and national research leaders, allowing rapid adoption of the results arising from this project. Similarly, the value for money of the project is high, as it leverages the currently high level of informatics capability available at EMR and sequencing and informatics capabilities at TGAC and provides a springboard to pan-European projects and industry-academia partnerships.

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 200.16K | Year: 2015

This project will support the development of a novel, portable and cost effective system for the detection of animal diseases in pigs. These diseases have a significant impact on animal health and represent a financial burden to countries worldwide. This collaborative project will deliver a magnetic sensor-based device and surveillance system which would provide early detection of disease and enable quick action in order to reduce the risk of disease spread, with economic benefits to farmers and food producers and welfare benefits to farm animals.

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