Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.1.2-03 | Award Amount: 6.90M | Year: 2014
WHEALBI will combine genomics, genetics and agronomy to improve European wheat and barley production in competitive and sustainable cropping systems. Germplasm representing the species diversity will be selected and characterised in unprecedented detail by next-generation-sequencing. Life history and adaptive traits will be evaluated in both transnational field experiments and a state-of-the-art precision phenotyping platform. Germplasm will be stored in a specialised and accessible bio-repository and associated data in knowledge bases that will represent a valuable legacy to the community. Whole genome association scans will be conducted for several traits, signatures of adaptive selection will be explored, and allele mining of candidate genes will reveal new variation associated with specific phenotypes. Pre-breeding tools and pipelines will be developed to optimize the efficiency of allele transfer from unadapted germplasm into elite breeding lines. New methodologies will explore how to optimally exploit the large amount of new genotypic and phenotypic data available. They will focus on the design of ideotypes with improved yield stability and tolerance to biotic and climatic stresses and provide proof of concept of the efficiency of genome and phenome assisted selection. Ideotypes and reference varieties will be evaluated in innovative cropping systems, particularly organic farming and no-till agriculture, and an economic evaluation of these approaches will be conducted. The results will be disseminated to a broad user community, highlighting the benefits and issues associated with the adoption of what is considered sustainable and environmentally friendly wheat and barley crop production in a European context. WHEALBI aims to help the EU remain a major actor in world small grain cereal production while addressing the pressing global priorities of increasing and stabilising primary production, improving food quality and safety, and reducing environmental impact.
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 459.43K | Year: 2017
Global demand for quantities of vaccines and therapeutic molecules is growing. Plants, in particular, are the source of a great diversity of biologically active small molecules and a great many natural products found in plants are used as human therapies. However, these chemicals are often found in low abundance or are produced in species that are difficult to mass-cultivate requiring either chemical synthesis or the transfer of the genetic pathway to an alternative biological host in order to produce compounds at sufficient quantities. While microorganisms have proven to be exceptionally powerful for manufacturing therapies, some are not easily produced in high yields. There is particular interest in platforms that are able to respond rapidly to new disease threats, for example, the production of vaccines. Plants have been shown to be capable of efficient expression of therapeutic proteins and secondary metabolites. In a process commonly known as molecular pharming plants have been demonstrated to be capable of producing a very large number of vaccine doses in just a few weeks. Gene expression can be complicated by the endogenous metabolism of the host diverting intermediates or performing unwanted modifications of expressed molecules. Much work has been done to tailor specific strains of bacteria and yeasts to increase production of compounds. However, to date, little effort has been spent on improving the plant production chassis, partly due to a lack of available tools. New technologies now allow us to take targeted approaches to modifying plant genes. We have identified genes expressed by the plant that are likely to be deleterious to heterologous bioproduction of small molecules. We will now make new lines of Nicotiana benthamiana, a relative of tobacco from Northern Australia, that are improved in their ability to produce small molecules of interest. We will then measure the impact of the changes that we have made by assessing the ability of our new lines to produce greater quantities of desirable new proteins and metabolites. This work will add to our knowledge of the metabolism of plants, helping us to understand how it responds to perturbation. It will also lead towards the production of plants that are genetically tailored for the production of different classes of therapeutic molecules
Agency: GTR | Branch: Innovate UK | Program: | Phase: Collaborative Research & Development | Award Amount: 475.09K | Year: 2015
This application is for funding to support the development of a novel, portable and cost effective system for the detection of animal diseases pigs. These diseases have a significiant impact on animal health and represent a financial burden to countries worldwide. If funded, this 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.
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: 749.69K | Year: 2016
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 150.96K | Year: 2017
Airborne crop diseases pose a serious threat to food security and are responsible for devastating loss of yield and over-reliance on pesticides. Early detection enables farmers to take preventative action, drastically reducing damage and cost. Current detection regimes often rely on expert identification of the pathogen from plant damage. More recently, other molecular techniques have emerged. However, these methods suffer the same problems - being specific for a single species and a need for relatively large quantities of pathogenic material. Recently, TGAC has been working on an approach dubbed Air-seq that seeks to identify pathogens through sequencing of biological particles present in air. This overcomes both problems associated with current techniques as it is unbiased (not limited by species) and requires very small quantities of material. Our ultimate aim is to put sample collection, sequencing and analysis in a single box that can be deployed in the field. Key to success is a compact sequencing technology and this has recently emerged in the form of Oxford Nanopore Technologies (ONT) MinION. The MinION is a new compact, low-cost sequencing technology that offers long reads (thousands of bases of DNA) and a streamed mode of operation enabling analysis of data as it is generated. These attributes make it ideally suited to in-field use. However, part of the process of generating sequencing data involves converting an electrical signal from the DNA sensing pore into a sequence of bases (letters) and this is performed via an internet basecalling service. For in-field deployment, this is unsatisfactory, as we cannot rely on high speed, reliable data connections. We believe a completely new approach is required in which we utilise the raw signal data in order to identify species, instead of searching against basecalled sequence. In this project, we will develop a tool that searches Nanopore signal data looking for the characteristic signal traces of pathogens of interest, building up a report on abundance levels in the process.
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: Research Grant | Award Amount: 119.19K | Year: 2016
Wheat is the most widely grown crop worldwide that provides 20% of the calories to the growing human population. It is estimated that the average person will consume the grain of 50 wheat plants per day (https://www.jic.ac.uk/calculations/), and to support this the UK exports 15-20% (~ 2m tonnes) of its yearly crop to over 20 countries worldwide , as well as providing for the UK market. Research into breeding programmes over the last decade has made large improvements in key traits such as yield, and growing ability in tough conditions for world market viability. It is strongly predicted that rapid climate change, newly emerging wheat diseases, and reliance on a small set of wheat varieties will greatly challenge modern day agriculture and food production. The availability of information about wheat genomes and the differences between them (variation) are leading a breakthrough in wheat research. Current services that share information about wheat genomes and these differences give researchers the ability to find regions of interest that match their research goals, and to understand and exploit characteristics of these regions for improving the crop. Such information can then be used in breeding programmes to design genetic markers for traits of interest, akin to marking Points of Interest on a map or navigation system. Once these markers have been discovered, robotic platforms can take this information and can screen thousands of wheat lines a day to look for matches, and hence potential knowledge about how that plant may perform in breeding experiments under different conditions. Tools and resources that harness the power of breeding data and analysis packages, both openly available to academics and industry alike, are key to accelerating wheat breeding programmes in the coming years. There are many web-based databases and information services that exist for housing and exposing wheat data. However, the stages leading up to screening the wheat lines involve intensive and laborious manual processes, and the availability of this information and the way it is represented is not consistent which makes it difficult for researchers and breeders to effectively utilise it for their research. Users must submit information at each step to multiple online or local analysis tools, run multiple queries and analyses, and manually process the results in desktop computer applications to ensure that they can be fed into the next tools in the workflow. Our project will remove these manual steps by developing software to automate the required interactions with commonly used online wheat data resources. As such, we will build software tools that are able to automatically connect each wheat data service in turn to form a workflow, understanding and processing the data produced by a previous service to provide the input data to the next service. This will free up valuable researcher time and, due to the removal of necessary human intervention and management of potentially complex data files, will result in a more robust and reproducible workflow.
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 767.42K | Year: 2016
The ELIXIR-UK Coordination Office, based at the Earlham Institute in Norwich, will provide national coordination for the activities of the UK Node of ELIXIR. ELIXIR is a European project to integrate life sciences data across the continent with the aim of facilitating the linking of data worldwide. Each country involved in ELIXIR has its own Node, the UKs Node being ELIXIR-UK. ELIXIR-UK coordinates a wide range of activities across training in bioinformatics, data integration, and provision of tools and data involving 16 UK Universities and Research Institutes and the Coordination Office will be pivotal in their delivery, cross-connectivity and impact.
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 436.31K | Year: 2016
Food security is internationally recognised as one of the major global challenges of the 21st century. By 2050, it is predicted that world food production will have to increase by 50% to meet demand. This is against the pressures of global climate change and resource limitations. Meeting this challenge is going to require the development of innovative strategies to make use of our unprecedented knowledge of modern bioscience in the post genomic era. Developing new varieties of wheat will be fundamental to meeting the 2050 goal. For wheat growers Internationally and specifically in India one of the key issues is drought. Drought means farms cannot always guarantee a good harvest with major implications for the livelihoods and household food security of small-holder farmers. Low rainfall also reduces the land area that can be farmed. Throughout the last century improvements in drought tolerance have come through breeding crops that grow in such a way that drought and drought sensitive stages of growth do not coincide. There is however, huge potential to breed new varieties capable of maintaining stable yields in drought conditions. In collaboration with the University of Bristol and the John Innes Centre (Norwich), work at the University of Liverpool has generated sequence data for the wheat genome. Using this information we have developed new methods to rapidly uncover the genetic variation in wheat. By combining an understanding of genetic variation with a careful study of performance under drought conditions it becomes possible to associate genetic variation with improved drought tolerance. Using this genetic information molecular marker tools cab be built, that can be used to rapidly select for lines that are drought tolerant. It is also possible to stack up multiple markers for different traits. As a consortium of interdisciplinary research scientists from the UK and India we plan to use this approach to identify molecular markers associated with drought tolerance in wheat and lay the foundations of an accelerated breeding program to incorporate drought tolerance into Indian wheat varieties. The approaches we will be using will provide a blueprint for how state-of-art technologies can be applied to important food security issues. Much of the output we generate can be used to identify markers for other traits. It will also result in highly trained researchers in India and the UK capable of applying these new approaches. Through outreach work we aim to engage with other researchers and stakeholders and apply this methodology to other traits in wheat and different crops.