Integrative bioinformatics platform, data integration and modelling
Lead Research Organisation:
Aberystwyth University
Department Name: IBERS
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Technological and analytical advances in plant science are increasingly data intensive. While this offers new opportunities for understanding plant biology and for precision plant breeding, it also brings challenges for data management and staff training. We propose to build a common platform for data analysis which will function across the Energy Grasses & Biorefining and Crop Genetics, Genomics & Germplasm ISPGs. The aim is to develop storage and archiving capacity and relational integration between datasets. Databases will be built to manage genomic and phenotypic data. These databases will complement the breeding database and visualisation system "MSCAN", a MySQL database system with a web-based interface. Software tools will be developed to allow cross database queries to retrieve data for analysis and visualisation. The aim is to promote synergistic activities within and across the ISPGs, with the wider research community and to enable the application of computational, mathematical and statistical tools to better understand the relationship of genotype, phenotype and the environment. Integrated datasets will be systematically analysed using bioinformatics, statistics and data mining methodologies to facilitate mass genotyping, and the identification of SNPs and other polymorphisms. We will use the informatics platform to identify ideotypes which combine optimum combinations of traits for different environments and end use. The crop models will allow analyses to predict the sensitivity of target traits under current and future climates. These outputs provide inputs for life-cycle and economic analyses, which will be linked right through to genotypes.
Planned Impact
unavailable
Publications
Clifton-Brown J
(2019)
Breeding Strategies to Improve Miscanthus as a Sustainable Source of Biomass for Bioenergy and Biorenewable Products
in Agronomy
Clifton-Brown, J
(2019)
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
in GCB Bioenergy
Davey CL
(2017)
Radiation capture and conversion efficiencies of Miscanthus sacchariflorus, M. sinensis and their naturally occurring hybrid M. × giganteus.
in Global change biology. Bioenergy
Harris Z
(2014)
Research Spotlight: The ELUM project: Ecosystem Land-Use Modeling and Soil Carbon GHG Flux Trial
in Biofuels
Hastings A
(2017)
Economic and Environmental Assessment of Seed and Rhizome Propagated Miscanthus in the UK.
in Frontiers in plant science
Hodgson E
(2016)
Horizon scanning the European bio-based economy: a novel approach to the identification of barriers and key policy interventions from stakeholders in multiple sectors and regions
in Biofuels, Bioproducts and Biorefining
Iqbal Y
(2017)
Harvest Time Optimization for Combustion Quality of Different Miscanthus Genotypes across Europe.
in Frontiers in plant science
Kalinina O
(2017)
Extending Miscanthus Cultivation with Novel Germplasm at Six Contrasting Sites.
in Frontiers in plant science
Lenk I
(2019)
Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon
in International Journal of Molecular Sciences
| Description | Data has been integrated and modelled to for example demonstrate the potential value of genomic selection as a tool to accelerate plant breeding in Miscanthus. A database has continued to evolve to not only store data but provide a visualisation tool for researchers and plant breeders. Data is being collected from Aberystwyth and also sites in other parts of the UK and Europe to enable studies of genotype x phenotype x environment interactions. This has necessitated the development and/ or implementation of associated data management technologies, for example bar coding, and tablets with phenotyping apps. |
| Exploitation Route | The information and tools developed are being tested experimentally in terms of how they can be used to acelerate plant breeding. Multisite field trials are providing data for modelling on the impact of climate change on future plantings of Miscanthus and to create greater yield stability. In November 2018, we (IBERS, Aberystwyth University) have submitted for Plant Variety Protection of our first four Miscanthus varieties (Artemis, Atropos, Astraea and Aphrodite) based on the results of recent trialling; a further four varieties were submitted for protection in 2019. This now means that our Miscanthus science has a route to market through a crop improvement pipeline to benefit UK farmers and be exported internationally. |
| Sectors | Agriculture Food and Drink Energy Environment Manufacturing including Industrial Biotechology Transport |
| Description | The information and tools developed are being tested experimentally in terms of how they can be used to acelerate plant breeding. Multisite field trials are providing data for modelling on the impact of climate change on future plantings of Miscanthus and to create greater yield stability. In November 2018, we (IBERS, Aberystwyth University) have submitted for Plant Variety Protection of our first four Miscanthus varieties (Artemis, Atropos, Astraea and Aphrodite) based on the results of recent trialling; a further four varieties were submitted for protection in 2019. This now means that our Miscanthus science has a route to market through a crop improvement pipeline to benefit UK farmers and be exported internationally. Data on GHG and soil carbon are providing information to industry on environmental impact of land use change involving energy grasses. Three Aberystwyth University postgraduates (2x PhD, 1x MSc), including those working on informatics are now working for UK bioenergy company Terravesta Ltd in Lincoln. |
| First Year Of Impact | 2015 |
| Sector | Agriculture, Food and Drink,Energy,Environment,Manufacturing, including Industrial Biotechology,Transport |
| Impact Types | Societal Economic |
| Description | BEACON+ Biorefining Centre |
| Amount | £8,000,000 (GBP) |
| Organisation | European Commission |
| Department | European Regional Development Fund (ERDF) |
| Sector | Public |
| Country | Belgium |
| Start | 06/2015 |
| End | 12/2019 |
| Description | MAGLUE Measurement and Analysis of bioenergy greenhouse gases: integrating GHGs into LCAs and the UK Biomass Value Chain Modelling Environment. |
| Amount | £993,785 (GBP) |
| Funding ID | EP/M013200/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2015 |
| End | 02/2018 |
| Description | Miscanthus UpScaling Technology (MUST) |
| Amount | £898,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2016 |
| End | 12/2018 |
| Description | Rural Development Plan; Plan Torri Tir Newydd |
| Amount | £295,284 (GBP) |
| Organisation | Government of Wales |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 11/2019 |
| Title | MiscanFor: A crop production model where Astley Hastings is the lead developer. |
| Description | MiscanFor (2009 to current day) is a crop model for projecting Miscanthus yield temporally and spatially using GXE data. MiscanFor has its roots in MISCAMOD (2004). |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2009 |
| Provided To Others? | No |
| Impact | It's an ongoing development led by my colleague Astley Hastings in Aberdeen |
| Title | Physis |
| Description | The Physis database has its roots in the IBERS database MSCAN. Physis is being developed by Michael Squance, a former IBERS PhD Student. Physis is designed to collect and collate standardized multi-location field trial data: plant performance (traits and yield), and environment (climate and soils). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The Physis system which began in Jan 2018, now includes mobile app and blue tooth technologies for efficient infield data collection. This is a game changer for a breeding research programme which requires long term, standardised data to improve models to project the regional production potential of seed based hybrids. |
| URL | http://physisdata.com/ |
| Description | Bioinformatics for crop genomics and breeding |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Data from field and phenomics and expertise on crop modelling and plant breeding. |
| Collaborator Contribution | Expertise on crop bioinformatics and data integration. |
| Impact | Work under progress on integration of bioinformatics for crop science and plant breeding. |
| Start Year | 2014 |
| Description | BBC Wales Science Cafe: The Welsh Science Wishlist |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | An interview for BBC Radio Wales Science Cafe. The programme was ahead of the Welsh Government Elections in May 2016 and was to articulate The Welsh Science Wishlist for the incoming government. Iain Donnison gave the interview on wishes for the future environmental policy. Science votes The Welsh Government believes that science in Wales is world class. And on this programme we frequently trumpet the pioneering research at our universities. But is enough being done to build a strong and successful scientific community? Many in Wales are concerned that we are failing on science education and in preparing for the digital future. In this special edition of Science Café scientists reveal, for the policy makers, their wish lists. And ahead of next month's elections, the political parties outline their scientific priorities. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.bbc.co.uk/programmes/b0776lxj |
| Description | Engagement with Young Farmers Groups |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Engagement through talks, tours and discussions with Young Farmers groups on what agricultural research is taking place at IBERS, Aberystwyth and how this can impact farming now and in the future. Requests for visits/ tours and for repeat visits from larger groups. |
| Year(s) Of Engagement Activity | 2013,2014 |
| Description | Miscanthus Safari |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | In November 2014 scientists, a Miscanthus Safari event was held to bring together policy makers and industry and funding bodies to hear the state of the art in Miscanthus research and to visit the extensive field trials established at Aberystwyth that contain the largest diverse collections of Miscanthus germplasm outside of Asia. The aim of the event was to highlight the progress that had been made over the last decade in the improvements in Miscanthus variety development and agronomy. In the previous 10 years a plant from the wild in Asia had been subject to modern biology and breeding approaches, to result in the trialling of experimental seed based hybrids being trialled by commercial partners on farms in the UK. This progress had only been made possible by the investment of public (principally BBSRC and Defra) and private funds. On the first day attendees visited the field sites to observe a range of activities from agronomic developments, new hybrid nurseries and large field scale analysis of carbon flux. The day was rounded off by a talk from a leading UK bioenergy crop company Terravesta on their work addressing technical and commercial barriers to large scale deployment of Miscanthus. The second day saw talks on diverse germplasm collections, developing new molecular technologies including genetic maps, germplasm and agronomic improvements for a maturing market, the environmental credentials of Miscanthus cultivation and matching land area and policy goals. The meeting emphasised the importance of biomass crops in helping moderate the effects of climate change and the short timescales over which such crops are required to deliver significant impacts. This challenge requires investment and progress to be made across a broad range of diverse research and commercial fields and was reflected in the diverse presentations across the two days. |
| Year(s) Of Engagement Activity | 2014 |
| URL | https://www.aber.ac.uk/en/news/archive/2014/11/title-159025-en.html |
| Description | Royal Welsh Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Annual displays and activities based on agriculature and environmental green issues, including on the planting of energy crops, non-food use of plants, use of grass to make ethanol and plastics. Activities sparked discussion with farmers, and public of all ages Visit to activities at Royal Welsh Show leads to subsequent requests for information and visits to IBERS in Aberystwyth. |
| Year(s) Of Engagement Activity | 2007,2008,2009,2010,2011,2012,2013,2014 |