Molecular Genetics of Miscanthus

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

The commercially grown variety of Miscanthus (M. x giganteus), is a naturally occurring triploid hybrid between M. sacchariflorus (4x) and M. sinensis (2x). The genetics of both parent species are being studied to evaluate the degree of diversity that exists in these and related species. The development and application of molecular biology and genomics technologies to Miscanthus is providing the basic genetic tools such as BAC libraries, transformation, and molecular markers for the development of genetic maps. These tools are required to associate genotype to phenotype for both performance and quality traits as part of fundamental research on complex traits in Miscanthus and also to underpin plant breeding. Candidate genes for yield and compositional associated traits, identified from the literature, databases, transcriptomic analyses and more targeted studies, will be mapped and related to quantitative trait loci (QTL) on the Miscanthus genetic map. The phenotype data is coming from the study of a diversity collection of 244 different genotypes. The genetic map and use of cross species markers will enable an estimate of the extent of synteny between Miscanthus and related C4 grasses including Sorghum, maize, switchgrass and sugarcane. The use of markers of known map position with other monocots will enable the use of implied QTL and candidate genes from the wealth of studies in C4 and other grasses. Association of phenotype to genotype is being performed in the diversity population and a mapping population created to study flowering time. New Miscanthus populations have and are being developed to study a wider range of traits. In addition Miscanthus transformation has been established and used to transform plants including with a Trichoderma risei ferulic acid esterase (FAE) gene.

Publications

10 25 50
 
Description IBERS with collaborators in Asia (including Toshihiko Yamada, University of Hokaido, Japan and Yu Chung Chang, Institute of Endemic Species, Taiwan) have built one of the, if not the, most extensive collections of Miscanthus in the world. This initially comprised a collection of approximately 300 accessions available in Europe, including from the European Miscanthus Improvement Network. The initial collection was partially assembled with Defra funding, and has been significantly expanded by subsequent collections from Asia (China, Japan, Korea and Taiwan) in 2006, 2007, 2008 and 2009 by IBERS and Ceres. The advantages of collecting ourselves has been that: accessions can be made which are targeted at biomass yield and other agronomic performance traits (most previous collections were made by taxonomists and horticulturists); phenotypic measurements can be made in the field under adaptive conditions; samples can be taken for chemical composition analysis; vegetative material can be taken from non-flowering genotypes; and full GPS co-ordinates of the collection site can be recorded to enable physio-geographic associations. IBERS is seeking to domesticate a new crop and therefore has placed significant effort into identifying the most appropriate germplasm. To understand the wild germplasm better, IBERS researchers organised a workshop on Miscanthus systematics in Taiwan which brought together experts from Kew and from across Asia to resolve a number of issues regarding nomenclature.
In 2005 a replicated diversity trial of 244 Miscanthus accessions was established at Aberystwyth. This was the only experiment of its type in Miscanthus when set up and has provided a valuable platform for research published from this project. IBERS have developed and applied a number of molecular genetic tools for the characterisation of grasses including BAC libraries, molecular markers, promoter analysis and mirco-arrays. This expertise was applied to Miscanthus, for example in the recent generation of high density SNP based genetic maps in Miscanthus in collaboration with Ceres Inc and on a BBSRC grant (BB/E014933/1). IBERS has also worked with TGAC on projects to sequence Miscanthus hybrids and high sugar perennial ryegrasses. IBERS researchers developed a transformation system for Miscanthus and have regenerated plants that express the Trichoderma rissei ferulic acid esterase (FAE) enzyme. This follows the successful expression within the ISP of FAE and xylanase in Festuca to manipulate fermentability.
Exploitation Route Characterisation of Miscanthus germplasm has been published and is being used by plant breeders including in the GIANT LINK project to improve Miscanthus. The first high density molecular marker map of Miscanthus was developed and published, and this information and knowledge is helping in the application of molecular markers to plant breeding to accelerate the rate of improvement. 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 Characterisation of Miscanthus germplasm has been published and is being used by plant breeders including in the GIANT LINK project to improve Miscanthus. The first high density molecular marker map of Miscanthus was developed and published, and this information and knowledge is helping in the application of molecular markers to plant breeding to acelerate the rate of improvement. 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 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 BBSRC Sustainable Bioenergy Centre (BSBEC)
Amount £5,259,854 (GBP)
Funding ID BB/G016216/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2009 
End 03/2015
 
Description Development of improved perennial non-food biomass and bioproduct crops for water stressed environments (WATBIO)
Amount £535,659 (GBP)
Funding ID 35358 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 11/2012 
End 10/2017
 
Description Energy Land Use Modelling (ELUM)
Amount £191,135 (GBP)
Funding ID ELUM 
Organisation Energy Technologies Institute (ETI) 
Sector Public
Country United Kingdom
Start 05/2011 
End 05/2014
 
Description Optimising Miscanthus Biomass production (OPTIMISC)
Amount £307,338 (GBP)
Funding ID 289159 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 10/2011 
End 03/2016
 
Description Optimization of Perennial Grasses for Biomass Production (OPTIMA)
Amount £129,799 (GBP)
Funding ID 289642 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 10/2011 
End 09/2015
 
Description Understanding processes determining soil carbon balance under perennial bioenergy crops.
Amount £80,000 (GBP)
Funding ID BBS/E/C00005071 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2009 
End 05/2014
 
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 BBC Wales Radio Science Cafe Programme 
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 Media (as a channel to the public)
Results and Impact Recorded discussion in a glasshouse growing Miscanthus

Increased awareness and programme was mentioned at subsequent interactions
Year(s) Of Engagement Activity 2009
URL http://www.bbc.co.uk/wales/radiowales/sites/sciencecafe/updates/20110809.shtml
 
Description Media interest in new genetic map in Miscanthus 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Broad range of interest from media and industry.

Interest generated in international media and with the associated research publication in PLoS One
Year(s) Of Engagement Activity 2013
URL http://www.bbc.co.uk/news/uk-wales-mid-wales-17402684
 
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, policy makers and representatives from industry and funding bodies gathered 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.
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. WATBIO research was presented by Dr Paul Robson who presented research from several groups across Europe toward improving the understanding of abiotic stress tolerance in Miscanthus to increase yield and the range of environments that can be used for Miscanthus cultivation.
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. Representatives from funding councils BBSRC and NERC, from companies, from government departments and academia left with the impression of a crop that was gaining impetus in addressing one of the world's big global challenges.
Year(s) Of Engagement Activity 2014
 
Description Renewble Transport Fuel Obligation 
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 Media (as a channel to the public)
Results and Impact Participation in Science Media Centre Press Release on "biofuels: are we asking the right questions?" to coincide with the UK Governments launch of the Renewable Transport Fuel Obligation

After the press release there were follow up calls and interviews on the use of plants and in particular grasses for energy including transport.
Year(s) Of Engagement Activity 2008
URL http://www.sciencemediacentre.org/biofuels-are-we-asking-the-right-questions/
 
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 Science Cafe talk and discussion on biofuels good or bad 
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 Talk sparked many questions and a long discussion

No immediate but subsequent reference to the engagement by some of those attending
Year(s) Of Engagement Activity 2010
URL http://www.ibers.aber.ac.uk/mailing_list/view_newsletter.asp?ID=42
 
Description Science Cafe talk and discussion on food vs fuel 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talk sparked many questions and a long discussion afterwards.

The discussion resulted in greater understanding of the broader and deeper implications by the audience and myself.
Year(s) Of Engagement Activity 2009
 
Description Skills Workshop on Phenomics and Metabolomics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The skills workshop took place on 11-12 September 2014 at Aberystwyth University in the UK. The aim of the workshop was to give participants practical experience of a number of phenomics and metabolomics analyses, and included demonstrations by a number of manufacturers attending to show new cutting edge technology in this field including the National Plant Phenomics Centre at Aberystwyth. The subject of the workshop was to provide researchers with an opportunity to increase and refine their knowledge of advanced phenomics with particular emphasis on getting first-hand experience of the advanced phenomics facilities at the newly opened UK National Phenomics Centre at Aberystwyth. Phenotyping is the cornerstone of genetic improvement through selection with breeders selecting desired strains by observing growth, vigour, incidences of disease etc. and of course yield. The workshop gave participants experience of modern precision phenotyping combining precise management of the plants' environment and advanced imaging to measure the responses of genotypes to different conditions. In addition to imaging, observations include sampling to examine the metabolic responses of plants were covered by the workshop thus linking the detailed observations of differences between plants to differences in the underlying genome.
Year(s) Of Engagement Activity 2014
URL http://www.watbio.eu/client/assets/media/pdfs/WATBIO_Skills_Workshop_on_Phenomics.pdf
 
Description WATBIO Stakeholder meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Multidisciplinary research was presented detailing, glasshouse, phenomics, modelling, molecular analysis and mapping populations used to improve understanding of water stress responses in Miscanthus. This research was presented to a mixed audience of academics, industry and representatives of the EU.
Year(s) Of Engagement Activity 2014,2015,2016,2017
URL http://www.watbio.eu/