Genetic resources for the dissection of bioenergy traits

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

The aim of the project is to provide genetic resources for the dissection of bioenergy traits. IBERS has assembled one of the world's largest collections of Miscanthus based on genetic resources already in Europe and its own extensive collections from Asia. This unique resource has already been used to make biparental mapping populations to identify QTL for flowering time, senescence and stem traits. Ongoing characterisations of germplasm are identifying a series of suitable new crosses including interspecific hybrids. These populations are being established for exploitation in other sub-programmes. To provide the plant materials to address biological and breeding questions in a perennial species such as Miscanthus, that takes several years before reaching maturity, requires significant planning. A number of new trials and populations are therefore being constructed to relate genotype to phenotype, genotype to environment, and phenotype to end use. These populations complement those established over the last eight years including an earlier diversity trial of Miscanthus genotypes that were in Europe prior to 2004, and mapping populations to study flowering time, leaf and stem traits.

Publications

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Bhatia R (2017) Genetic engineering of grass cell wall polysaccharides for biorefining in Plant Biotechnology Journal

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Clifton-Brown (2015) History of the development of <em>Miscanthus</em> as a bioenergy crop: from small beginnings to potential realisation in Biology and Environment: Proceedings of the Royal Irish Academy

 
Description 1) New genetic resources have been developed for Miscanthus research including the assembly of i) a diversity population of 1000 plants in triplicate, ii) ten mini-mapping populations in triplicate, and two larger mapping populations of up to 1000 individuals. This combined with next generation sequencing (RAD-Seq) has allowed the development of pipelines for genetic mapping and comparative genomics.
2) With partners using DNA based molecular markers we have created a dense DNA based molecular marker map in Miscanthus, and identified 90 quantitative trait loci (QTL) for 26 of 32 scored bioenergy traits spanning field performance, chemical composition and release of sugars.
Exploitation Route Research is being used to help UK industry move to seed based hybrid production of Miscanthus. Progress has also been made on implementing UN protocols for the Convention on Biological Diversity and Access and Benefits Sharing. These are some of the first examples for new (non-staple) crops. 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. 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 Knowledge gained in the ISPG has been applied for Miscanthus hybrid seed production in southerly latitude in Italy and planted on demonstration farms in the UK by Terravesta Ltd. This has led to an Agri-Tech grant (MUST) and the technology demonstrated by Terravesta on their stand at the Cereals Event. We have also implemented the United Nations Protocols for the (Rio) Convention on Biodiversity and (Nagowa) Access and Benefit Sharing enabling commercial use of genetic resources and creation of impact from BBSRC science. In May 2012, Taiwan was the first Asian country to sign a full Access and Benefit Sharing agreement under the Convention on Biodiversity framework with the UK, followed in March 2013 by South Korea. These are some of the first examples for new (non-staple) crops. Novel IBERS seed-based Miscanthus varieties are now being trialed on farms in the UK and across Europe. 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. 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.
Sector Agriculture, Food and Drink,Energy,Environment,Manufacturing, including Industrial Biotechology,Transport
Impact Types Societal,Economic

 
Description Fair and equitable use of natural resources through development of Miscanthus as an industrial crop
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact Through our research and implementation of an international conservation policy, the United Nation's Convention of Biological Diversity (CBD), we have achieved an impact toward the implementation of public policy at the global-scale for the conservation of genetic resources. The CBD entered into force on 29 December 1993 following the United Nations Conference on Environment and Development (the Rio "Earth Summit"). The Convention was inspired by the world community's growing commitment to sustainable development and represented a dramatic step toward the conservation of biological diversity, the sustainable use of its components, and the fair and equitable sharing of benefits arising from the use of genetic resources. New crop breeding programmes are dependent on the collection and characterisation of diverse genetic resources. Importantly since the domestication of the staple crops, legally binding contracts including the CBD have been put in place to ensure that where genetic resources are collected from one country and commercially exploited elsewhere, the benefits of the exploitation are shared with the donor country. IBERS researchers pioneered the making of new Miscanthus collections and the negotiation of the necessary agreements in the absence of clear national legislation for the implementation of the access and benefit sharing arrangements under the CBD and ahead of the implementation of the Nagoya Protocol on Access and Benefit Sharing in 2011. IBERS scientists worked closely with Defra and partners in Asia to implement the CBD and access and benefit sharing Protocols through organising joint workshops, collaborative research and legal negotiations. For example an international Workshop on Green Chemistry and Biomass Energy which was jointly funded by the National Science Council of Taiwan and the BBSRC, was held at the National Cheng Kung University on 3 November. Aberystwyth University and National Cheng Kung University formally signed a memorandum of understanding at the workshop, the signing of which was presided over by the vice chancellor of the Cheng Kung University and the CEO of BBSRC. In May 2012, Taiwan was the first Asian country to sign a full access and benefit sharing agreement under the CBD framework with the UK, and this was followed by successful negotiations with South Korea with an agreement to comply with CBD in November 2011, negotiations for access and benefits sharing up to July 2013 and an official signing of access and benefits sharing in October 2013. On both occasions the UK was represented by BEAA in the negotiation. This has created one of the first examples for implementing Nagoya protocols in the UK and our partnering countries. Not only have IBERS scientists implemented two international agreements but their experience and knowledge of setting up bi- lateral access and benefit sharing agreements under the CBD framework is now also being used as a proven example for others to follow, helping to support government's approach to legislation in this area. This includes the UK government's approach to the proposed "Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization (Nagoya Protocol): Union implementation and ratification", an EU-wide legislation to be submitted to the European Parliament which was voted on in committee on 4 July 2013. The main beneficiaries of this policy impact are therefore the UK government's agriculture policy legislation body (Defra), donor countries in Asia, commerce (only compliant germplasm can be commercially exploited in signatory countries) and the global society on the conservation of natural resources.
 
Description Participation in BEIS consultation on the Bioeconomy
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description AgriTech; Miscanthus Upscaling Technology (MUST)
Amount £901,884 (GBP)
Funding ID BB/N016149/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2016 
End 01/2019
 
Description BEACON+ Biorefining Centre
Amount £8,000,000 (GBP)
Organisation European Commission 
Department European Regional Development Fund (ERDF)
Sector Public
Country European Union (EU)
Start 07/2015 
End 12/2019
 
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 Real time control of gasifiers to increase tolerance to biomass variety and reduce emissions
Amount £999,756 (GBP)
Funding ID EP/M01343X/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 03/2015 
End 03/2018
 
Description UK BBSRC ERA-NET Bioenergy
Amount £544,779 (GBP)
Funding ID BB/K021591/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2013 
End 08/2016
 
Title Miscanthus endophytic bacteria collection 
Description Collection of bacterial strains isolated from Miscanthus tissues 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact Published 2017. In use in on-going research. 
URL http://onlinelibrary.wiley.com/doi/10.1111/gcbb.12364/pdf
 
Description Miscanthus genome 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Miscanthus genome 
Organisation HudsonAlpha Institute for Biotechnology
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Miscanthus genome 
Organisation Teagasc
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Miscanthus genome 
Organisation U.S. Department of Energy Joint Genome Institute
Country United States 
Sector Public 
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Miscanthus genome 
Organisation University of California, Berkeley
Country United States 
Sector Academic/University 
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Miscanthus genome 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data
Collaborator Contribution Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers
Impact Publication in preparation
Start Year 2014
 
Description Structural polymorphisms as causes of heterosis in Populus 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution Data analysis expertise on genome-wide trait prediction
Collaborator Contribution A unique set of data on structural DNA polymorphisms in large populations
Impact Promising early results on genome-wide prediction using structural polymorphisms.
Start Year 2014
 
Description Structural polymorphisms as causes of heterosis in Populus 
Organisation West Virginia University
Country United States 
Sector Academic/University 
PI Contribution Data analysis expertise on genome-wide trait prediction
Collaborator Contribution A unique set of data on structural DNA polymorphisms in large populations
Impact Promising early results on genome-wide prediction using structural polymorphisms.
Start Year 2014
 
Description Articles for Biochemical Society's blog 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Experience communicating with a wider audience about the experience of being a PhD student and the research project. Raise awareness of the research group.
https://thebiochemistblog.com/2017/05/18/phyte-club-inside-the-plant-microbiome/
https://thebiochemistblog.com/2017/03/27/the-very-best-things-about-phd-life/
Year(s) Of Engagement Activity 2017
URL https://thebiochemistblog.com/2017/05/18/phyte-club-inside-the-plant-microbiome/
 
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 BBSRC's Bioenergy Public Dialogue 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Activity generated a lively discussion

Participants asked many questions and greatly increased their knowledge about bioenergy
Year(s) Of Engagement Activity 2013
 
Description British Science Week 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 2016 - PhD students presented a poster of their research project with an audience of school children and teachers. Posters were later copied and sent to teachers for display in schools.
Students from 9 Secondary schools were in attendance over the course of the week.
2017 - PhD students organised and ran a stand for the three day event, supervising a team of undergraduate students.
• A three day event demonstrating chemical changes and properties to early secondary school aged children from several local schools using hands-on experiments they could try.
• Voted third place out of around 40 different stands at the event.
• Over 3000 schoolchildren attended over the event.
• Video online including PhD student talking about endophytes https://www.aber.ac.uk/en/news/archive/2017/03/title-198574-en.html
Year(s) Of Engagement Activity 2016,2017
URL https://www.aber.ac.uk/en/news/archive/2017/03/title-198574-en.html
 
Description Cereals event 
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 with farmers and growers on the potential use of Miscanthus on farms in the UK and the delivery pipeline for seed based varieties, including on the potential environmental benefits on marginal low carbon soils. This including raising awareness of the availability of seed based Miscanthus hybrids and their significant advantage over rhizome based M. x gianteus in terms of cost of establishment, scaleability and disease susceptability.

More farmers aware of Miscanthus as an option and the improvements that are in the pipeline
Year(s) Of Engagement Activity 2012,2013,2014,2015
 
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 Genomics-assisted breeding 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Generated keen interest and discussion with Wales Young Farmers Clubs visitors

Several visitors expressed interest in learning more about my research
Year(s) Of Engagement Activity 2013
 
Description Invited presentation (Slavov): Bioenergy Genomics 17 Oxford Conference. Integrated genomic prediction in bioenergy crops. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Generated discussions and outlined future research with peers working in bioenergy crops.
Year(s) Of Engagement Activity 2017
URL http://www.watbio.eu/bioenergy-genomics-17-oxford-conference/
 
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 Panel discussion at Energy Now Expo, Telford 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk sparked questions and led to subsequent new industry collaboration
Year(s) Of Engagement Activity 2014
URL http://content.yudu.com/Library/A26a45/EnergyNowEXPO2013/resources/index.htm?referrerUrl=http%3A%2F%...
 
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
 
Description Segment on BBC news 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interviewed for Welsh language news segment. Recently for a section on women in science, previously for a segment about renewable energy
Year(s) Of Engagement Activity 2014,2016
URL http://www.bbc.co.uk/iplayer/episode/p03fd8qc/newyddion-9-s4c-pennod-19
 
Description Slavov (cross-institute BBSRC workshop on predictive breeding) 
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 Explored potential for developing a cross-institute (Roslin, Earlham, JIC, NIAB, RRes, IBERS ...) ISP on predictive breeding. A report was submitted to BBSRC outlining next steps / key questions.
Year(s) Of Engagement Activity 2018
 
Description Slavov (invited presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Multi-omic dissection and prediction of complex traits in plants. XIV International Symposium on Integrative Bioinformatics, Harpenden, UK, June 14, 2018
Year(s) Of Engagement Activity 2018
URL https://www.rothamsted.ac.uk/events/14th-international-symposium-integrative-bioinformatics
 
Description Talk at 4th International Symposium of Forage Breeding, Melbourne, Australia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Talk sparked discussions among academics and industry participants.

Talk sparked discussions among academics and industry participants and led to new collaborations in Australia.
Year(s) Of Engagement Activity 2013
 
Description Talk at PlantSci 2012; the UK Plant Sciences Federation Inaugural Research Conference, Norwich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Talk sparked questions and social media discussion
Year(s) Of Engagement Activity 2013
 
Description Various student engagement activities 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact IBERS Excellence with Impact Poster session. 28th April 2016
• Presenting a poster of my research plans as part of the IBERS EWI event
• 80-100 people attended the event.
Presentation to School Teachers. 8th June 2016
• A ten minute oral presentation of research project to secondary school teachers.
• 20-30 teachers were in attendance.
Public Engagement Poster Session. 18th June 2016
• Presented a research poster to an audience of the general public.
• Over 100 people attended
World Food Day poster. 16th October 2016
• Public outreach event marking World Food Day, organised and hosted with fellow postgraduate students.
• The event illustrated the journey of food from production, through processing, to consumption, and waste, and highlighting environmental impacts.
• ~50 people attended.
Science and Energy Lecture. 19th May 2017
• Delivering a 2 hour lecture to primary school children on energy changes, with hands on demonstrations of a range of experiments.
• Groups from three primary schools were in attendance, totalling over 80 children.
• There will hopefully be a repeat of this event 2018.
Worcester Postgraduate Research Conference 29th June 2017
• 15 minute oral research presentation to a conference session of academic researchers and other postgraduate students from a range of disciplines and institutions.
• 80-100 people were at the event.
Online Outreach
• Blog (friendlybacteria.wordpress.com) writing about Science (mainly microbiology) for a general audience. I'm not sure how many people this has reached.
• Social Media: use of Instagram to post about Science and Nature (@friendly_bacteria) and Twitter to do the same (@frndlybacteria). Over 500 followers on Instagram and nearly 1300 on Twitter.
Year(s) Of Engagement Activity 2016,2017