Resilient Crops: Crop Genomics
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
Crop genomics: Building on reference genomes now available for our crop species we will integrate existing and novel - omics data to understand the genomic transcriptomic and epigenomic contributions to resilience in individuals and hybrids. IBERS gene bank contains thousands of accessions of forage grasses clover oats and Miscanthus with details of where they were collected. We will use this crop biodiversity resource to increase our understanding of the genomic diversity within each crop to enable discoveries of gene function genotype by environment interaction hybridisation/introgression potential and value for use in plant breeding programmes.
Planned Impact
unavailable
Organisations
- Aberystwyth University (Lead Research Organisation)
- International Institute of Tropical Agriculture (Collaboration)
- University of Illinois at Urbana-Champaign (Collaboration)
- HudsonAlpha Institute for Biotechnology (Collaboration)
- U.S. Department of Energy Joint Genome Institute (Collaboration)
- QUEEN'S UNIVERSITY BELFAST (Collaboration)
- Agricultural University of Iceland (Collaboration)
- National Botanic Garden of Wales (Collaboration)
- UNIVERSITY OF READING (Collaboration)
- International Crops Research Institute for the Semi-Arid Tropics (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- Agriculture and Agri-Food Canada (Collaboration)
- University of Florida (Collaboration)
- University of California, Berkeley (Collaboration)
- Teagasc (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
Publications
Abd El-Daim IA
(2024)
Halotolerant bacterial endophyte Bacillus velezensis CBE mediates abiotic stress tolerance with minimal transcriptional modifications in Brachypodium distachyon.
in Frontiers in plant science
Davies J
(2024)
Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed
in Environmental Microbiology Reports
Ellis N
(2023)
Recombinant inbred lines derived from wide crosses in Pisum.
in Scientific reports
Freeland L
(2024)
Precision Breeding and Consumer Safety: A Review of Regulations for UK Markets
in Agriculture
Gangashetty PI
(2023)
Genotype-by-environment interactions for starch, mineral, and agronomic traits in pearl millet hybrids evaluated across five locations in West Africa.
in Frontiers in plant science
Gutierrez N
(2024)
Genome-wide association study for yield-related traits in faba bean (Vicia faba L.)
in Frontiers in Plant Science
Jellen E
(2024)
A uniform gene and chromosome nomenclature system for oat (Avena spp.)
in Crop & Pasture Science
Khatri K
(2023)
Functional genomic and transformation resources for commercially important red macroalgae (Rhodophyta)
in Algal Research
| Description | Hosted visit from DESNZ staff at IBERS |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Presented written evidence to Welsh Government committee regarding the Genetic Technology (precision breeding) bill brought forward by the UK Government |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Delivering low glycaemic index (GI) pearl millet grains for the benefits of type-2 diabetics in African regions |
| Amount | £331,655 (GBP) |
| Funding ID | 105672 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2019 |
| End | 03/2022 |
| Description | Ensembl Plant Populations: integrating trait analyses and population-based sequence variants into a browsable genomic context |
| Amount | £1,250,000 (GBP) |
| Funding ID | BB/X018725/1 |
| Organisation | National Institute of Agronomy and Botany (NIAB) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 09/2026 |
| Description | International Science Partnership Fund (HEFCW) |
| Amount | £39,000 (GBP) |
| Organisation | Higher Education Funding Council for Wales (HEFCW) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2024 |
| End | 02/2025 |
| Description | Lucky and resilient: Genomic improvement of cold tolerance in red and white clover |
| Amount | £125,000 (GBP) |
| Funding ID | 2929096 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2024 |
| End | 09/2028 |
| Description | Miscanspeed |
| Amount | £2,083,436 (GBP) |
| Organisation | Government of the UK |
| Department | Department for Business, Energy and Industrial Strategy |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 03/2025 |
| Description | PeaProtein: Breeding peas for the plant-based protein market |
| Amount | £755,704 (GBP) |
| Funding ID | 10046667 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| Title | Genomic marker panel for Miscanthus |
| Description | Cost-effective Flex-seq marker panel developed for Miscanthus sinensis and Miscanthus sacchariflorus to enable large-scale screening of Miscanthus populations, e.g. for genomic selection. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Genomic selection, coupled with speed breeding, reduces each Miscanthus breeding cycle from 3 years to 1, thereby accelerating the generation of new varieties for sustainable biomass production. Using these markers we have implemented GS in Miscanthus sinensis and Miscanthus sacchariflorus for the first time. |
| Title | Plant-associated bacteria |
| Description | Bacterial collections have been made from plants and their immediate environments |
| Type Of Material | Biological samples |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Not yet fully exploited or published |
| Title | 16s Microbiome dataset |
| Description | The data consist of the 16s sequences for the rhizosphere microbiome of plant model Brachypodium distachyon |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | The main impact was identifying how the Brachypodium distachyon rhizosphere microbiome assembly is responding to inoculation with beneficial microbes under different environmental conditions |
| Title | Geographic coordinates of Populus Trichocarpa genets used in common gardens established and maintained by the Center for Bio energy Innovation. (CBI) |
| Description | This data set contains the geographic coordinates of the GWAS population described in Tuskan et. al, 2011 and Evans, et. al, 2014. These genotypes have been used in numerous experiments since then, and have been propogated in common gardens. The most recent common garden geo referenced dataset for Davis, California is also available. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This data set contains the geographic coordinates of the GWAS population described in Tuskan et. al, 2011 and Evans, et. al, 2014. These genotypes have been used in numerous experiments since then, and have been propogated in common gardens. The most recent common garden geo referenced dataset for Davis, California is also available. Tuskan G, Slavov G, DiFazio S, Muchero W, Pryia R, Schackwitz W, Martin J, Rokhsar D, Sykes R, Davis M, Studer M, Wyman C. Populus resequencing: towards genome-wide association studies. BMC Proc. 2011 Sep 13;5(Suppl 7):I21. doi: 10.1186/1753-6561-5-S7-I21. PMCID: PMC3239865. Evans, L., Slavov, G., Rodgers-Melnick, E. et al. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46, 1089-1096 (2014). https://doi.org/10.1038/ng.3075 |
| URL | https://www.osti.gov/biblio/1969513 |
| Title | MxG transcriptomic response to drought and flooding PRJEB86745 |
| Description | 105 RNAseq libraries exploring the transcriptomic response of Miscanthus x giganteus to early or late drought and flooding stresses on controlled conditions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Collaboration between IBERS and EI demonstrates the complementary skills of both institutes. This project fits into the interest on expression dynamics on hybrid allopolyploids. The results will help design biomarkers, better understand the biology of the commercial Mxg cultivar, and feed into future research on stress priming and epigenetics. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB86745 |
| Title | PRJEB57630: Haplotype-resolved assembly and annotation of Trifolium pratense cv. Milvus using HiFi long-reads and 10X linked-reads |
| Description | We assembled the complete 18 chromosomes of a heterozygous genotype of the outcrossed species Trifolium pratense |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Enhancing red clover's role in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with the model legume Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes in red clover, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. |
| Title | Pipeline to phasing and scaffolding heterozygous outcrossed polyploid and diploid genomes based on pruning Hi-C data |
| Description | The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline tailored to the polyploid genomes and tested it to anchor the tetraploid genome of Brachiaria decumbens cv. Basilisks that we previously sequenced with HiFI. We also generated Hi-C reads for the red clover cultivar cv. Milvus that we sequenced using HiFi reads in a previous funding scheme. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline tailored to the polyploid genomes and tested it to anchor the tetraploid genome of Brachiaria decumbens cv. Basilisks that we previously sequenced with HiFI. We also generated Hi-C reads for the red clover cultivar cv. Milvus that we sequenced using HiFi reads in a previous funding scheme. |
| Title | Sequencing multiparental nested population: four families and 480 red clover offspring |
| Description | Progeny, 4 subfamilies, ~100 individuals/family: 480 progeny at 1X (5x LITE plates and 1x S4 Novaseq, ENQ5122). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | Because genotyping is cheaper the lower is the coverage needed, an underlying question for population genotyping using WGS is on the minimum coverage needed for accurate haplotype calling. A particularly challenge at low coverages is calling homozygous sites; i.e., if the alternative allele is not observed, is it because it does not exist or are not there enough reads?. A solution is for the progeny's haplotypes to be inferred or imputed on the accurate allelic information stored in the progenitors' pangenome. |
| Description | Collaboration between ISPs: DECODE and Resilient Crops (monthly meeting) |
| Organisation | Aberystwyth University |
| Department | Institute of Biological, Environmental and Rural Sciences (IBERS) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Monthly online meeting between staff and students between both institutes working in IBERS' WP4 or EI's WP2 ISP objectives. There were kick-off visits to both IBERS and EI from the respective ISP leads. EI hosted IBERS' ISP PI (KF) during a 3 day visit. We agreed shoared objectives on clovers, ryegrass, Miscanthus and oats pangenomics that reuse tools and knowhow generated in DECODE. |
| Collaborator Contribution | Monthly online meeting between staff and students between both institutes working in IBERS' WP4 or EI's WP2 ISP. We hosted IBERS' ISP PI (KF) during a 3 days visit, and agreed a follow-up visit to identify further areas of coordination between both ISPs. |
| Impact | TBD |
| Start Year | 2023 |
| Description | DNA barcoding in grassland swards |
| Organisation | National Botanic Garden of Wales |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Collaboration on the DNA barcoding of grassland species, including those planted and those recruited from the seed bank. This includes a grazing and cutting study at four diverse sites across an altitudinal challenge gradient at the Trawsgoed and Pwllpeiran farm sites ranging from 70m to 340m above sea level. |
| Collaborator Contribution | Our partners at NBGW have assisted in the development and optimisation of protocols for the analysis of farmed and natural (weed) grassland species. |
| Impact | The outcomes are under development but will help in the understanding of, and therefore advice that can be given for, the management of grassland mixtures in both lowland and upland environments |
| Start Year | 2023 |
| Description | DTP FoodBiosystems PhD Studentship. 2020-2024 100 years of plant breeding - what have we done to the seed microbiome? |
| Organisation | University of Reading |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Farrar leads the Agricultural Sciences and the BioEconomy theme in IBERS, AU, comprising 27 PIs plus associated staff and students. She has published over 30 papers on plant development, energy crops and plant-microbe interactions. She has successfully supervised six PhD students to completion, with four ongoing (one submitted, awaiting viva); of these, 4 projects have been in collaboration with industrial partners or public bodies. Dr Catherine Howarth is a Reader at AU and leads the Cereals and Pulses Group. Her research focuses on understanding the control of agriculturally important traits and the incorporation of these traits into improved plant varieties. She has experience in managing a number of large multidisciplinary projects including collaborations with industry and has successfully supervised 4 PhD students to completion. |
| Collaborator Contribution | Richard Ellis is Professor of Crop Production, UoR. His research spans agronomy, crop phenology, and anhydrous biology in relation to environment, including climate change impacts. He has expertise in the effect of environment on seed production, on seed storage survival, and on germination for application in the global network of genebanks (ex situ biodiversity conservation for crop plant breeding) and to crop establishment. In anhydrous biology more widely, he has researched fungal spore survival for biological control. He is PI of the National Fruit Collection in Kent, a Director of the World Vegetable Center, and has successfully supervised 43 PhD students to completion. Alexey Mikaberidze is a lecturer in Crop Protection, UoR. His interdisciplinary research combines mathematical and computational modelling with multi-scale experimentation and he is an expert within analysing diverse large-scale datasets. |
| Impact | 'Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed' accepted for publication in Environmental Microbiology Reports. No DOI yet. |
| Start Year | 2020 |
| Description | DTP FoodBiosystems PhD Studentship. 2020-2024 Identifying beneficial plant-microbial interactions using multi-omic approaches |
| Organisation | Queen's University Belfast |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Kerrie Farrar works on plant-microbial interactions, her work underpins this project. Her group is contributing microbial strains, experimental and genomic data as well as expertise. Dr Swain is trained in Physics and Computing science. He joined IBERS in 2011 as a Bioinformatics Lecturer. He currently coordinates bioinformatics activity in IBERS, including managing computing infrastructure. He has successfully supervised 1 M. Phil and 1 PhD studentship to completion, and is currently the main supervisor of three ongoing Ph.D. projects (one student has submitted) and co-supervisor of another PhD student (who has also submitted). Over the last 5 years he has published over 30 papers on the genomics of microbes, parasites, plants and animals. He has previously worked with the co-supervisor, Dr Cameron, successfully publishing an article. |
| Collaborator Contribution | Dr Cameron specialises in microbiology and mass spectrometry metabolomics. He joined QUB as a Vice-Chancellor's Fellow (lecturer-equivalent position) in 2019 after completing a PhD at Aberystwyth University and Post-Doctoral research work at Imperial College London in mass spectrometry instrumentation development. At QUB, Dr Cameron is building a research group that applies microbiology and metabolomics to the study of early life nutrition and maintains active research in the use and development of the REIMS technology that will be employed in this project. |
| Impact | The student is currently taking time out for personal reasons. |
| Start Year | 2020 |
| Description | DTP FoodBiosystems PhD Studentship. 2023- New software to detect horizontal gene transfer in microbiomes: from forage to the rumen |
| Organisation | Queen's University Belfast |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Kerrie Farrar has an ongoing collaboration with Dr Martin Swain on the bioinformatics of plant-microbial interactions. Dr Farrar leads the plant and microbial work and Dr Swain leads the informatics. This is the second DTP PhD studentship we have co-supervised. Dr Farrar has contributed microbial strains, experimental and genome data. |
| Collaborator Contribution | Professor Creevey (QUB) is a computational biologist with an interest in applying ecological and evolutionary principals to microbial communities. The research in the group primarily focusses on bioinformatic analyses, including the development of novel open source computational approaches for evolutionary analyses and understanding microbial community organisation and structure. |
| Impact | Too soon |
| Start Year | 2023 |
| Description | Genomic prediction by modelling genotype by environment interaction for yield in groundnut |
| Organisation | International Crops Research Institute for the Semi-Arid Tropics |
| Country | India |
| Sector | Charity/Non Profit |
| PI Contribution | The main aim of this collaboration was to understand the extend of genotype by environment interaction in groundnut breeding programs. We used datasets from Malawi and Uganda in our study. Nelson Lubanga helped in the designing and execution of this project. Nelson Lubanga co-ordinated all the processes including data analysis, presentation and also drafted a manuscript that is currently under review titled "Genomic prediction by modelling genotype by environment interaction for yield in groundnut": https://doi.org/10.1101/2024.10.30.621054 |
| Collaborator Contribution | Damaris Odeny (ICRISAT) - Provided the data and reviewed the manuscript. Nelson Lubanga (Aberystwyth University) - design, data analysis, presentation, manuscript preparation and submission for publication. Diego Jarquin (University of Florida) - design, analysis and review of the manuscript. |
| Impact | This project led to the development of a paper that is currently under peer review. |
| Start Year | 2024 |
| Description | Genomic prediction by modelling genotype by environment interaction for yield in groundnut |
| Organisation | University of Florida |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The main aim of this collaboration was to understand the extend of genotype by environment interaction in groundnut breeding programs. We used datasets from Malawi and Uganda in our study. Nelson Lubanga helped in the designing and execution of this project. Nelson Lubanga co-ordinated all the processes including data analysis, presentation and also drafted a manuscript that is currently under review titled "Genomic prediction by modelling genotype by environment interaction for yield in groundnut": https://doi.org/10.1101/2024.10.30.621054 |
| Collaborator Contribution | Damaris Odeny (ICRISAT) - Provided the data and reviewed the manuscript. Nelson Lubanga (Aberystwyth University) - design, data analysis, presentation, manuscript preparation and submission for publication. Diego Jarquin (University of Florida) - design, analysis and review of the manuscript. |
| Impact | This project led to the development of a paper that is currently under peer review. |
| Start Year | 2024 |
| Description | Island Oats |
| Organisation | Agricultural University of Iceland |
| Country | Iceland |
| PI Contribution | new collaboration on developing oats for Iceland and understanding the physiology of key traits |
| Collaborator Contribution | Field trials and networking meeting established |
| Impact | Succesful application to NERC Arctic Networking Call |
| Start Year | 2024 |
| Description | Miscanthus genome, pangenome |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | HudsonAlpha Institute for Biotechnology |
| Country | United States |
| Sector | Charity/Non Profit |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | Teagasc |
| Country | Ireland |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| 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 | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Sparse testing designs for optimizing resource allocation in multi-environment cassava breeding trials |
| Organisation | International Institute of Tropical Agriculture |
| Country | Nigeria |
| Sector | Charity/Non Profit |
| PI Contribution | Nelson Lubanga was involved in designing this project. The main aim of this project was to reduce the cost of setting up multi-location trials using sparse testing. Nelson Lubanga co-ordinated all the activities involved including convening of regular meeting, data analysis, presentation and writing of a manuscript that was eventually published in a high impact journal: https://doi.org/10.1002/tpg2.20558 |
| Collaborator Contribution | IITA provided the datasets that were used for the analysis. Nelson Lubanga (Aberystwyth University) helped in the designing of this project, data analysis and leading the writing of the manuscript. Diego Jarquin (University of Florida) helped in the designing and analysis of the project. |
| Impact | Through this collaboration, we published a paper titled "Sparse testing designs for optimizing resource allocation in multi-environment cassava breeding trials": https://doi.org/10.1002/tpg2.20558. This collaboration was multidisciplinary as it involved plant breeders (Ismail Rabii), Biometricians (Ibnou Dieng), quantitative geneticists (Nelson Lubanga) and statisticians ( Diego Jarquin). |
| Start Year | 2024 |
| Description | Sparse testing designs for optimizing resource allocation in multi-environment cassava breeding trials |
| Organisation | University of Florida |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Nelson Lubanga was involved in designing this project. The main aim of this project was to reduce the cost of setting up multi-location trials using sparse testing. Nelson Lubanga co-ordinated all the activities involved including convening of regular meeting, data analysis, presentation and writing of a manuscript that was eventually published in a high impact journal: https://doi.org/10.1002/tpg2.20558 |
| Collaborator Contribution | IITA provided the datasets that were used for the analysis. Nelson Lubanga (Aberystwyth University) helped in the designing of this project, data analysis and leading the writing of the manuscript. Diego Jarquin (University of Florida) helped in the designing and analysis of the project. |
| Impact | Through this collaboration, we published a paper titled "Sparse testing designs for optimizing resource allocation in multi-environment cassava breeding trials": https://doi.org/10.1002/tpg2.20558. This collaboration was multidisciplinary as it involved plant breeders (Ismail Rabii), Biometricians (Ibnou Dieng), quantitative geneticists (Nelson Lubanga) and statisticians ( Diego Jarquin). |
| Start Year | 2024 |
| Description | TUGBOAT-ICEBREAKER |
| Organisation | Agriculture and Agri-Food Canada |
| Country | Canada |
| Sector | Public |
| PI Contribution | Provide genetic material (both varieties and mapping populations) for cold tolerance screening and genotyping. |
| Collaborator Contribution | Genome analysis and phenotyping |
| Impact | Too early to report |
| Start Year | 2024 |
| Description | BBSRC Seeding award dissemination event, AgriTech-E |
| 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 | Presentation and display of the results from BBSRC Seeding Award. Has led to collaboration with new industry partners and a number of grant proposals including one with INnovate UK which has subsequnetly been funded |
| Year(s) Of Engagement Activity | 2023 |
| Description | Biomass and Energy Crops VI |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Hosted the Biomass and Energy Crops VI workshop at Aberystwyth University, on both the Penglais and Gogerddan campuses. The workshop brought together the international community including from Europe, North America and Asia with workshop presentations and included site visits to IBERS field plots, phenotyping, seedbank and biorefining facilities. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.aab.org.uk/event/biomass-and-energy-crops-vi/ |
| Description | Cereals 2023 |
| 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 | PeaGen project poster displayed on PGRO stand at annual Cereals event. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Chair annual Bioenergy Grass Genomics workshop, Plant and Animal Genome meeting, San Diego |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Kerrie Farrar runs an annual workshop at the Plant and Animal Genome meeting in San Diego every January. This workshop, co-chaired by Kankshita Swaminathan of Hudson Alpha, USA, brings together the international perennial bioenergy crop community. This has previously resulted in the Miscanthus genome publication and more recently USA-UK grant applications. |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024 |
| Description | Conference presentation at the Plant and Animal Genome Conference - San Diego |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presenting results form the ISPG project entitled 'Adopting DNA metabarcoding in grassland systems' as part of the Forage, Feedstocks & Turf workshop. This conference presentation facilitated the establishment of valuable connections with international researchers. Subsequent meetings and discussions have been conducted since to source funding opportunities to establish future collaborative research partnerships between the Institute of Biological, Environmental, and Rural Sciences (IBERS) and the Department of Biological Sciences at the University of Alberta, Canada. |
| Year(s) Of Engagement Activity | 2024 |
| Description | DOE Resilient Bioenergy Crop Production Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participated as an international expert in the US DOE Resilient Bioenergy Crop Production Online Workshop over 3 days to identify future research challenges, opportunities and priorities. This was followed by giving a presentation at the Lawrence Livermore National Laboratory in January 2025. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.genomicscience.energy.gov/pre-meeting-feedback-resilient-bioenergy-crop-production-works... |
| Description | Engagement with Farmers Unions |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Delegations from the Farmers Unions and other stakeholders visit IBERS on a regular basis. Recent examples where Miscanthus research has been the focus of conversation include: FUW Presidents visit to IBERS Gogerddan, 22nd November 2023 NFU Cymru President and Director visit to IBERS Gogerddan, 7th March 2023 NFU Cymru Next Generation, visit to IBERS Gogerddan, 15th February 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Harnessing Innovation, the future of biomass |
| 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 | The Harnessing Innovation, the future of biomass event, hosted by Biomass Connect, showcased the latest innovations in biomass production and processing emerging from the Biomass Feedstocks Innovation Programme and included presentations and practical workshop sessions from a wide range of speakers from all areas of the biomass industry. The event included an exhibition of planting machinery, aeroponics, decision support tools, breeding advances and other innovations from across the biomass supply chain. The event aimed to showcase progress and explore the process of continuing funding for the innovations supported under the Biomass Feedstocks Innovation Programme. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.biomassconnect.org/showcase-event/# |
| Description | Invitation as a facilitator for the Training Workshop on "Genomic Selection (GS) for Dryland Crops (DC)", at ICRISAT, Hyderabad, India, February 03-07, 2025. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nelson Lubanga was invited as a subject matter specialist and one of the facilitators of the Training Workshop on "Genomic Selection (GS) for Dryland Crops (DC)" took place in Hyderabad, India from February 03-07, 2025. The purpose of the workshop was to share knowledge on the implementation of GS, identify potential entry points for breeders of different dryland crops, and to use their own datasets to streamline and optimize ongoing GS programs. A group of 50 participants including plant breeders, bioinformaticians and biometricians attended this workshop. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.icrisat.org/storage/file-managers/file-67248ad93351e4.86635420.pdf |
| Description | Keynote, UK Legume Conference 2024; "Adaptations and admixture in common bean and genomics for breeding" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Keynote speaker in the Genomics and Genetics session of the UK Legume Conference in Reading, 14-15 Feb 2024 |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://uklrc.org/uklrc2024/ |
| Description | Low Carbon Agriculture Show 2023 (Stoneleigh) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Produced media, (banners and handouts) for stall manned for 2 days to engage with attendees. Questions on use and availability of Miscanthus crop plus impacts on co-benefits including flood mitigation and end uses such as biochar. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Nelson Lubanga was invited as a presenter at the Plant and Animal Genome conference (PAG) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nelson Lubanga presented at the Plant and Genome conference in San Diego, California, USA in 2024. The title of the talk was Genomic Prediction Using Sparse Testing for Multi-Environment Miscanthus Trials. During this conference, Nelson Lubanga was able to meet key collaborating partners in ICRISAT and IITA. Nelson Lubanga has already drafted two papers using IITA and ICRISAT datasets. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Oat pangenome workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Three day workshop, consisting of a closed meeting for members of the PanOat consortium on day 1, a broader open meeting presenting cereal genomics related topics on day 2 and a networking day on day 3. BBSRC funding supported facilities and hospitality to allow attendance by colleagues from US and Europe as well as a number of UK institutions. In person and virtual presentations described a broad range of public or collaborative resources, from databases and bioinformatics tools to genotyping platforms and genetic resources. Industry, research and infrastructure groups presented and participated in discussions. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation on Oat Genetic Diversity at 2nd Food Oats Conference Lund, Sweden |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Initiated new collaborations |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://foodoatsconference.com/ |
| Description | Radio interview for Radio Wales on the role of AI in plant breeding |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Iain Donnison and Gancho Slavov took part in a discussion broadcast on Radio Wales 'Science Cafe' programme on the role of AI in plant breeding. This related to the application of AI to net zero and the development of Miscanthus varieties for greenhouse gas removal. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.bbc.co.uk/programmes/m001qt9m |
| Description | Royal Society Innovating Agriculture event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participated and chaired an expert panel on ": How can innovations in food and agriculture be deployed at scale?" at the Royal Society Innovating agriculture event. This was part of the conference series "Transforming our future" and explored the science and innovation aiming to transform the future of food and farming. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://royalsociety.org/-/media/about-us/industry/tof-conference-reports/transforming-our-future-in... |
| 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 | Industry/Business |
| Results and Impact | Project flyer displayed on the IBERS stand at the 2023 Royal Welsh Show, 24th - 27th July, Builth Wells. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Wales Innovation Network/Wales Higher Education Brussels event, Brussels, 28 Feb, 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Farrar showcased IBERS' Miscanthus research at the WIN/WHEB event 'Welsh universities research excellence in partnership: Opportunities on the Horizon'. The Wales Innovation Network and Welsh Higher Education Brussels, in partnership with Universities Wales and Global Wales, hosted an exhibition of Welsh research and innovation as part of the St David's Day Brussels 2024 programme. The aim was to offer an opportunity to gain insight into developments in the Welsh research and innovation landscape through discussions with academics and university leaders, with a focus on our commitment to European collaboration as we fully engage with the Horizon Europe programme. Miscanthus research was selected as a leading example of of innovative projects contributing to Net Zero. Rt Hon Mark Drakeford MS, First Minister for Wales was the keynote speaker. Dr Farrar spoke with him about the role Miscanthus can play to help Wales reach its goals, including the benefits of perennial biomass crops to decarbonise heavy industry and to substitute for tree planting, with additional benefits for the farmer. There was a diverse guest list including numerous science and innovation networks. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Wales Innovation network, London |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Kerrie Farrar showcased IBERS' Miscanthus research at a reception in Lancaster House, London, 17th Oct, 2023. The Wales Innovation Network (WIN) and the office of the Secretary of State for Wales held a joint reception to showcase the strengths and breadth of Welsh research and innovation, including on Net Zero and Decarbonisation, to UK politicians, civil servants and funders. The Miscanthus research was selected from a longlist within Aberystwyth University. Speakers and attendees from UK Government included: • Rt Hon David TC Davies MP, Secretary of State for Wales • George Freeman MP, Minister for Science, Research and Innovation |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.aber.ac.uk/en/news/archive/2023/10/title-267312-en.html |