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Resilient Crops (Earlham Institute)

Lead Research Organisation: EARLHAM INSTITUTE

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

The overall objective of the Institute Strategic Programme Grant (ISPG) “Resilient Crops” is to support agricultural productivity by ensuring the stability of yield and quality of perennial ryegrass clover oats and Miscanthus. By so doing we aim to tackle the challenges associated with making agriculture more resilient to climate change and more sustainable enabling it to contribute to Net Zero solutions. A primary objective of the ISPG is to increase basic knowledge of key traits relating to the consistency of yield and quality across environments and seasons including extreme weather events. This is particularly important for perennial crops. “Resilient Crops” aims to create and utilize tools that will aid in delivering our scientific findings and speed up the process of developing new crop varieties. The ISPG is organised into four work packages; this project (work package 4) “Crop genomics underpinning adaptation diversity and regulation” will integrate existing and novel omics data for our crop species to understand the genomic transcriptomic and epigenomic contributions to resilience in individuals and hybrids.

Planned Impact

unavailable
 
Description EI's unique capabilities, large-scale genomics, and toolkit improvements from DECODE (EI's ISP) help address questions about how complex genome-wide variation influences traits in agriculture and aquaculture production systems. This supports Resilient Crops' goal of filling knowledge gaps in resilience and resource use efficiency in forage, grain, and energy crop science by leveraging the innovative genetic resources, experimental platforms, and expertise available at IBERS.

Both Institutes are collaborating on three joint projects. The distinct strengths of each institute are showcased through our specific joint initiatives. These efforts cannot be completed by a single ISP alone, as they require the combined expertise and resources, as we aim to emphasise here:
(1) We aim to improve the persistence of white clover. Nearly 200 accessions from genebanks across Europe, notably including many materials from the IBERS' genebank, were compiled into a diversity panel by IBERS. This panel has been established in two trials at IBERS, with phenotyping scores collected over a two-year period (ongoing work). Concurrently, the panel has been genotyped using EI's cost-effective in-house library protocol, LITE2, to produce a comprehensive sequencing dataset. This dataset is currently under analysis at EI and through a secondment between the institutes.
(2) We aim to clarify the transcriptional dynamics of the commercial Miscanthus hybrid cultivar. IBERS conducted and sampled a detailed stress time-course experiment involving multiple genotypes and combined drought and waterflooding stresses. EI then created a dataset comprising 105 RNA-seq libraries, which is currently being analysed at EI. Re-annotation of the Miscanthus genome has been performed at EI and shared among partners. This dataset is currently under analysis at EI.
(3) To determine the species-wide genetic diversity of ryegrass, IBERS collected a range of accessions representing the latitudinal and longitudinal distribution of ryegrass in southern Europe, which was then sequenced at EI. The genomes of these 10 accessions have been assembled and analysed for gene and protein diversity by IBERS, using EI's HPC resources.
Exploitation Route Population-scale analyses of white clover and regulatory elements in Miscanthus can help breeders and genomics researchers identify candidate regions associated with resilience traits and adaptive alleles.
Sectors Agriculture

Food and Drink
 
Description Our work enables more precise identification of candidate regions that underpin resilience and adaptation, thereby strengthening the evidence base for breeding decisions and the design of follow-up studies. Translation progresses through active partnerships with industry (e.g., Germinal), which offer an immediate pathway to discovering trait-associated markers and predictive breeding pipelines.
First Year Of Impact 2025
Sector Agriculture, Food and Drink
Impact Types Economic
 
Description BBSRC (FoodBioSystems DTP): CASE PhD studentship
Amount £119,760 (GBP)
Funding ID FBS2024-045-Lloyd-ac 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2024 
End 09/2028
 
Description Boosting innovation in breeding for the next generation of legume crops for Europe
Amount £319,250 (GBP)
Funding ID 101081329-2 
Organisation European Commission 
Sector Public
Country Belgium
Start 03/2023 
End 09/2027
 
Description Boosting innovation in breeding for the next generation of legume crops for Europe
Amount £368,936 (GBP)
Funding ID 10077978 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2023 
End 02/2028
 
Description Earlham Institute and Tozer Seeds Limited KTP 23_24 R5
Amount £176,013 (GBP)
Funding ID 10102570 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 07/2024 
End 02/2027
 
Description Engineering Ecosystem Resilience through the lens of genomic technologies
Amount £16,632 (GBP)
Organisation Advanced Research and Innovation Agency (ARIA) 
Sector Public
Country United Kingdom
Start 09/2025 
End 01/2026
 
Description Germplasm relevant to DAC-listed countries
Amount £495,000 (GBP)
Funding ID BBS/OS/GC/000011A 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 07/2017
 
Description John Innes Foundation internship in data-driven plant bioinformatics
Amount £38,000 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2021 
End 08/2023
 
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 Summer studentship
Amount £4,208 (GBP)
Organisation University of East Anglia 
Sector Academic/University
Country United Kingdom
Start 05/2024 
End 08/2024
 
Title AI models for seed species classification 
Description we have developed two segmentation pipelines: one AI-based (Cellpose v4) and another using classic image analysis techniques (ImageJ), to generate single-seed masks for each seed starting from scanned images of seeds scattered across a domestic flatbed scanner. Then, we used an ImageJ (Schneider et al., 2012) plugin (Loddo et al. 2023) to extract numerical values for 64 features regarding the colour, texture and shape features of each seed. In parallel, we developed a Python script using OpenCV v2 to generate individual seed squared images from the masks to use with image-based classification models. We compared over 20 ML and DL classification models for tabulated phenotype scores, as well as image-based CNNs. 
Type Of Material Data analysis technique 
Year Produced 2026 
Provided To Others? Yes  
Impact This study presented methods for classifying wildflower seeds using image analysis and AI. The optimal method depends on the balance between accuracy and computational time, the use of AutoML tools, and whether the classification involves a closed set of species. If the focus is on absolute metrics without regard for computational cost, neural networks for segmentation (CellPose) and classification (ResNet50) proved to be the best options. However, generating tabulated features was an order of magnitude faster than deep learning segmentation. In closed-set classification, the complex models from AutoGluon were the most accurate, but four models from vanilla scikit-learn performed similarly. In open-set classification, Random Forests clearly excelled because of their transparent use of calibration and thresholds to assign unseen species to the unclassified class. Our findings indicate that traditional machine learning models, such as random forests and gradient boosting, achieve high classification accuracy with lower computational demands than deep learning methods. Nonetheless, our extended analyses also demonstrated that deep learning (ResNet50) can achieve almost perfect accuracy when supplied with high-quality segmentation (e.g., Cellpose), offering a pathway towards fully automated image-to-classification pipelines at a higher computational cost. 
URL https://github.com/DeVegaGroup/SeedClassifier
 
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 on white clover molecular breeding with Germinal GB Ltd 
Organisation Germinal
Country United Kingdom 
Sector Private 
PI Contribution Improving the persistency of white clover through three objectives: (1) Exploring diversity panel using landscape genomics, population analysis (2) GWAS with persistency traits from GWAS trial (3) Unlocking persistency-related traits from Caucasian clover
Collaborator Contribution Germinal is providing cash contribution and supervision of PhD student, supporting summer placements
Impact I have done one summer visit (investigating Caucasian hybrids and trial design).
Start Year 2024
 
Description Collaboration with data management working group (Lars-Otto Gernot and Ivo Rieu) for Legume Generation 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects.
Collaborator Contribution They have assisted in maintaining standards at other partner institutes and providing input to us in ways to standardise procedures
Impact We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects.
Start Year 2024
 
Description Collaboration with data management working group (Lars-Otto Gernot and Ivo Rieu) for Legume Generation 
Organisation Radboud University Nijmegen
Country Netherlands 
Sector Academic/University 
PI Contribution We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects.
Collaborator Contribution They have assisted in maintaining standards at other partner institutes and providing input to us in ways to standardise procedures
Impact We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects.
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 Tozer Seeds Knowledge Transfer Partnership 
Organisation Tozer Seeds
Country United Kingdom 
Sector Private 
PI Contribution Develop a project idea for a Knowledge Transfer Partnership (KTP) with Tozer Seeds, management of the application process and negotiation of IP and terms. The KTP will help Tozer to develop internal capacity to analyse genomic data for accelerated breeding. This collaboration began as a service provided by NBRI1 and JV in 2022, after which the BDI team assisted in developing it further into the KTP.
Collaborator Contribution Tozer co-applied for KTP with EI and will be providing funding and in-kind support.
Impact Application for a KTP submitted in November 2023. Earlham Institute gaining status as a KTN Knowledge Base. KTP was funded and started in July 2024 and will run till December 2026 (30 months)
Start Year 2022
 
Title Basecall2Assembly: v1.0 basecall and error correction pipeline for Nanopore Q20 reads 
Description Accurate basecalling of ONT nanopore reads is crucial for generating reliable and high-quality sequencing data for downstream analyses. Our SNAKEMAKE pipeline takes POD5 files with raw signals from the sequencer and generates corrected reads ready for haplotype-aware assembly. 
Type Of Technology Software 
Year Produced 2025 
Open Source License? Yes  
Impact In Oxford Nanopore Technology (ONT) sequencing, basecalling is the process of converting the electrical signals generated by DNA passing through a nanopore into a nucleotide sequence, while HERRO is a haplotype-aware error correction tool that improves the accuracy of ONT reads, particularly for ultra-long reads. HERRO uses a two-stage approach: all-vs-all alignment followed by haplotype-aware correction using a deep learning model, which helps to improve single-read accuracy. HERRO can improve the accuracy of ONT reads, leading to better genome assemblies and analyses. 
URL https://doi.org/10.5281/zenodo.15005310
 
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 Presentation at Eucarpia Fodder Crops and Amenity Grasses Conference (2025 September) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This is an biannual conference which bring together more than 100 forage breeders and researchers from across the Europe to share the cutting-edge breeding technologies, recent breakthrough in forage breeding and blueprint future vision in the field. We had presentation sessions for most important temperate forages (clovers, alfalfa, ryegrass etc). I had a 20-minute presentation about what has been done for white clover genomic breeding between Earlham Institute and Germinal. There were plenty of networking events with breeders from different countries, providing opportunities for potential collaboration and resource-sharing for developing more sustainable and climate-resilient forages. There was also on-site visit to IBERS (Institute of Biological, Environmental and Rural Sciences at Aberystwyth University) and Germinal, which was perfect to knowledge sharing in forage breeding field.
Year(s) Of Engagement Activity Pre-2006
URL https://www.forages-eucarpia.org/fcag-section-meeting-2025/
 
Description Save the Banana! at the Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We took an activity aimed at 4-10 year old children to Norwich Science Festival 2024. This activity was based around the De Vega group's work on banana genomics. Over the three days we attended the festival we engaged with more than 1000 children and feedback (measured via feedback forms) was very positive. Many participants did not know the Cavendish banana was under threat.
Year(s) Of Engagement Activity 2024
 
Description Visit and workshop of EI researchers to IBERS. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Crop Genomics - Earlham Institute visit to IBERS 20th July 2023
Year(s) Of Engagement Activity 2024