Integrative bioinformatics platform, data integration and modelling

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

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.

Publications

10 25 50

 
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 Participation in BEIS consultation on the Bioeconomy
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description BEACON+ Biorefining Centre
Amount £8,000,000 (GBP)
Organisation European Commission 
Department European Regional Development Fund (ERDF)
Sector Public
Country Belgium
Start 07/2015 
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