Dr Jose De Vega

I am a Group Leader (tenured) at the Earlham Institute, Norwich, UK. I lead a multidisciplinary research programme in crop genomics, genetic variation and genome evolution, combining genome assembly, population and pangenomics, quantitative genetics, high-throughput phenotyping and predictive approaches to understand complex genomic variation and translate it into crop improvement.

Alongside my research programme, I lead and co-lead major national and international collaborations spanning BBSRC institutes, CGIAR centres and commercial breeding partners. These include leadership roles in Legume Generation, DECODE and CELLGEN, consortia, with organisations including CIAT, ILRI, IRRI and RBG Kew, and crop improvement partnerships with Tozer Seeds, Germinal Horizon and Tropic Biosciences. My responsibilities span scientific strategy and delivery, researcher development, budgets, reporting, recruitment and coordination across partner organisations. Increasingly, my work also involves the delivery of community-facing resources, tools and FAIR data infrastructure, connecting data with analysis and practical use by breeders.

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Current role and scientific leadership

Since June 2022, I have been a Group Leader at the Earlham Institute. Before this, from September 2017 to June 2022, I was an Earlham Institute Fellow developing genomic approaches to improve crop adaptation and resilience, including work within the Global Challenges Research Fund GROW Colombia programme.

I currently coordinate DECODE WP2 and Legume Generation WP7, serve as deputy coordinator for CELLGEN WP2, and lead externally funded research and knowledge-exchange projects. Across these programmes, I contribute to scientific delivery, budgeting, recruitment, reporting and coordination with internal and external partners.

Scientific expertise

My scientific background spans more than a decade of computational genomics applied to crop and plant science. A recurring theme is understanding complex genetic variation and its consequences for phenotype, adaptation and breeding. This ranges from SNPs and haplotypes to structural variants, copy-number changes, introgressed regions and homoeologous exchange, particularly in hybrid and polyploid crops where single-reference and SNP-centred analyses often fail to represent the full diversity available to breeding.

Earlier in my career at EI, I managed the genome projects for red clover, Brachiaria/Urochloa and Miscanthus. My independent programme has subsequently expanded from reference-genome generation towards population genomics, pangenomics and the integration of genomic and phenotypic variation in crops including banana, rice, common bean, tropical forages, clover and vegetables.

This progression from reference genomes to richer representations of diversity is exemplified by our current white clover work with Germinal Horizon and IBERS, where we are developing multiple high-quality assemblies and a pangenome to capture genetic diversity relevant to environmental adaptation and breeding.

Plant–pathogen interactions provide another important translational strand. Our banana research uses genomic diversity in cultivated bananas and their relatives to identify potential sources of resistance to Fusarium TR4, working in collaboration with Tropic Biosciences and combining experimental disease assays with genome analysis and candidate-gene discovery. My research also extends to the crop–insect pest interface, using genomic and quantitative-genetic approaches to understand crop responses to economically important pests in tropical improved forage grasses

I am particularly interested in AI where it can improve biological interpretation, genomic analysis, data curation, prediction or user-facing research tools. I have hands-on experience applying machine learning and deep learning, including use of scikit-learn and PyTorch for classification and predictive problems in plant science. Our recent AI work on biological classification compared conventional machine-learning and deep-learning approaches while considering computational cost, robustness and practical deployment.

Genomic resources and research infrastructure

An increasing component of my work concerns the transition from analysing datasets within individual research projects to developing resources through which wider communities can discover, integrate, analyse and reuse genomic and phenotypic information.

A major example is the Horizon Europe Legume Generation programme. I am one of the research institute leads and co-lead Work Package 7, which is developing the project’s digital Knowledge Centre and Legume Discovery platform. Legume Generation brings together partners across Europe and internationally, including research organisations, breeding programmes and commercial partners. The Earlham Institute is responsible for integrating phenotypic and genetic information generated across the consortium and making these resources accessible to breeders and other stakeholders. More detail on this activity is available in Boosting beans for breeders and Standout innovation contributes to knowledge exchange.

A dedicated analytical module supports multi-environment trial analysis, applying mixed-linear models and calculating BLUEs and BLUPs across locations and seasons. Alternative models can be compared so that users can evaluate their performance before selecting outputs. Backend development is extending the platform towards marker-data management, GWAS integration and marker-to-target discovery.

This is also reflected in my role within the BBSRC Decoding Biodiversity (DECODE) programme. I lead the EI activity on genetic diversity in agri/aquacultural traits, where we investigate introgression, chromosomal rearrangements and structural variation as sequencing moves from single reference genomes towards multiple high-quality assemblies and long-read population resources.

People leadership and researcher development

Developing researchers is a central part of my role. I have supervised two PhD students to completion and am primary supervisor for two further PhD students. I also serve as secondary supervisor for four PhD students. Since January 2026, I have served as Postgraduate Researchers Director at EI in a shared role, with responsibility for overseeing the academic progression and support of more than 30 postgraduate researchers. This involves ensuring effective monitoring and support mechanisms, working with students and supervisors where intervention is required and contributing to the quality of the wider postgraduate research environment. I am also a member of the NBI Graduate School Executive.

I use undergrad internships (Msc and BSc) as genuine research and training opportunities rather than isolated short projects, and we are open to student enquiries. Students work on defined scientific questions, receive appropriate independence and are encouraged to communicate and publish useful outputs. Our recent AI work, for example, grew through a series of undergraduate projects in which successive interns contributed to development and benchmarking of machine-learning approaches.

Research programmes, grants and project leadership

My research programme has been supported through competitive funding from UKRI/BBSRC, Horizon Europe, Innovate UK, ARIA, the British Council, the Royal Academy of Engineering, and other national and international programmes.

Current and recent awards and leadership roles include:

  • PI: Building environmental resilience through the lens of genomic technologies (ARIA, 2025–2026)
  • PI: Knowledge Transfer Partnership with Tozer Seeds to advance and integrate genomic technologies into vegetable breeding (Innovate UK, 2024–2026)
  • Co-I and WP lead: Legume Generation: Boosting innovation in breeding for the next generation of legume crops for Europe (Horizon Europe, 2023–2028)
  • Co-I and WP lead: BBSRC Institute Strategic Programme Decoding Biodiversity (DECODE) (2023–2028)
  • Co-I / deputy WP lead: BBSRC Institute Strategic Programme Cellular Genomics (CELLGEN) (2023–2028)
  • PI / CASE supervisor: PhD projects in white clover, banana and common bean
  • PI and Co-I on earlier projects spanning crop biodiversity, digital infrastructure, forage genomics, rice genomics, sugarcane breeding and biodiversity-based bioeconomy initiatives in Colombia, Peru, Vietnam, Kenya and the UK.

These roles cover the grant lifecycle from programme development and proposal writing through recruitment, scientific and financial management, delivery, reporting and collaboration with research, grants, contracts and finance teams.

International, CGIAR and breeding partnerships

Collaboration across institutes, countries and sectors is a central feature of my research.

I have longstanding relationships with international agricultural research organisations, including CIAT, ILRI and IRRI, connecting genomic research with crop and livestock-production challenges in Latin America, Africa and Asia.

Our tropical forage research, for example, has involved collaboration with CIAT and ILRI to develop genomic resources and breeding tools for Urochloa/Brachiaria, crops that are important to livestock production across tropical regions. This work has included genome resources, genetic maps, population and quantitative genomics and marker development for breeding.

My earlier work on rice crops in a changing climate similarly connected large-scale genomic diversity with breeding and conservation, while also supporting international training and capacity building.

A major focus of my current work is collaboration with commercial breeders and biotechnology companies:

  • With Germinal Horizon and IBERS, we are developing genomic resources and a white-clover pangenome to understand cold adaptation and support breeding of resilient forage varieties: Unlocking the agricultural value of clover.

  • With Tozer Seeds, I lead a Knowledge Transfer Partnership embedding genomics directly within a commercial vegetable-breeding programme. Our work on resilient celery connects genomic diversity, disease resistance and practical breeding requirements.

  • With Tropic Biosciences, we investigate genomic diversity and resistance to Fusarium TR4 in banana, combining fundamental genomics with routes towards resistant commercial material: Bananas are on the brink but close cousins could save their skins.
  • Through Legume Generation, I work with a large international network of research institutes and commercial breeding programmes to make phenotypic and genetic information accessible and analytically useful for breeders.

Knowledge exchange and industry

The Tozer Seeds KTP is a particularly direct example Knowledge exchange is integral to my research rather than a downstream activity: it places a computationally and genomically trained researcher between the Earlham Institute and a commercial breeding programme, with the aim of transferring and embedding approaches that can accelerate breeding decisions.

Our work within Legume Generation similarly connects research infrastructure directly with its users. The project integrates data from field trials and genetic markers and makes these data and analytical outputs accessible to breeders and stakeholders for use in breeding decisions.

I have also developed funded collaborations with Tropic Biosciences, contributed to commercial service activities through Earlham Enterprises and presented translational work through EI Innovate, NRP Agri-Tech and related events.

Training and community engagement

I have a longstanding interest in connecting bioinformatics, genomics and breeding through training.

I organised the Earlham Institute’s Bioinformatics for Breeding course, designed for breeders, pre-breeders and bioinformaticians interested in applying genomic methods to crop improvement. The practical programme covered HPC and command-line analysis, SNP discovery and variant context, genetic maps, high-throughput phenotyping, GWAS, genomic prediction and genomic selection.

This type of training reflects an important part of my approach to community engagement: analytical methods and resources have greater impact when users understand their assumptions, limitations and practical applications.

I have also contributed to Software and Data Carpentries training and helped organise a Virtual Summer School in HPC, bioinformatics and data science in Colombia, supporting capacity building and widening access to computational genomics.

My teaching and training experience additionally includes invited lecturing, postgraduate and MSc supervision, undergraduate research projects and paid summer internships.

Employment history

Earlham Institute, Norwich, UK

  • 06/2022 – present: Group Leader

Earlham Institute, Norwich, UK

  • 09/2017 – 06/2022: Fellow
    Genomic approaches to crop adaptation and tolerance to climate change, including research within GROW Colombia.

Earlham Institute, Norwich, UK

  • 05/2013 – 09/2017: Postdoctoral Researcher
    Comparative and crop genomics, including management of the red clover, Brachiaria/Urochloa and Miscanthus genome projects.

ITQB, Lisbon, Portugal

  • 07/2010 – 05/2013: Postdoctoral Researcher
    Transcriptomics in pine and oak during embryogenesis.

University of Salamanca, Spain

  • 06/2009 – 07/2010: Research Assistant
    Molecular plant–pathogen research, greenhouse experiments and molecular biology.

Education

  • PhD in Agronomic Biotechnology, University of Salamanca, 07/2009
    Fusarium oxysporum–Phaseolus molecular interactions and Fusarium wilt

  • BSc in Environmental Sciences, University of Salamanca, 09/2004

Scientific and academic service

My invited talks and scientific presentations span crop diversity and evolution, pangenomic tools and workflows, legume and forage genomics, adaptation and admixture in common bean, genetic variation and applications of genomics to crop resilience and sustainable agriculture.

I contribute to the wider scientific community through peer review and research assessment. I have reviewed grants for BBSRC and NERC, am a member of the NERC Peer Review College, and have also reviewed proposals for international research councils.

Internally, I contribute to PhD recruitment and project-selection panels for the BBSRC Norwich Research Park Doctoral Training Partnership and the NERC ARIES Doctoral Training Partnership.

At institute and partnership level, I represent EI on the ARIES DTP Board and have represented the Institute or Faculty on committees concerned with Horticultural Services and New Infrastructure, Inclusivity, Diversity, Equality and Accessibility (IDEA), and Information Systems and Library.

I also coordinate scientific interactions with IBERS, including joint deliverables, shared programme objectives, collaborative PhD projects and cross-institute genomics meetings.

Public engagement and broader service

I contribute to public communication around crop genomics, genetic diversity, food security and climate resilience.

Examples include work on orphan crops and food security, biodiversity and the genetic integrity of restoration material, and the role of genomic diversity in making crops more resilient.

I helped develop and deliver the “Save the Banana” activity for the Royal Norfolk Show and Norwich Science Festival, based around the genetic vulnerability of clonally propagated banana crops. The activity has subsequently been reused at multiple events.

I have also served as a judge at the enviroSPRINT event organised by four NERC Doctoral Training Partnerships, supporting early-career researchers developing translational ideas in environmental science.

Beyond research and training, I have contributed to policy and public affairs through service on a consultative panel supporting the UK’s position on digital sequence information on genetic resources in the context of the Convention on Biological Diversity. This complements my wider interest in the governance, openness and responsible reuse of genomic information.