We are working to create genomic resources and to breed for increased photosynthetic efficiency in the African orphan leafy crop Cleome gynandra. This work is a collaboration between Niab, the University of Cambridge (the Department of Plant Sciences and the Crop Science Centre) and the University of Abomey-Calavi, Benin.
2022-2027
To be marketed and/or awarded Plant Breeders Rights (PBR) in the UK, all agricultural varieties must pass DUS (Distinctness, Uniformity and Stability) testing. This ensures that new varieties are unique, with distinctness determined by visually comparing candidate varieties against other varieties in common knowledge (the ‘variety collection’).
In this Defra-funded project we are exploring ways to accelerate variety registration using genomic prediction approaches. Working on barley, we are refining and optimising our machine learning prediction models, focussed on prediction of individual barley DUS characteristics (phenotypes), to facilitate earlier selection of similar varieties from the variety collection for field distinctness assessments. Predictions models are being tested in parallel to current DUS testing procedures, with consideration of logistical and technological challenges for future implementation. Software for user-implementation of the finalised models is also being developed to support the use of the analysis pipeline by DUS testing centres.
September 2025-March 2028
Nature has already run millions of evolutionary “experiments.” By analysing ancient environmental DNA, AEGIS will identify lost genetic traits, ancestral diversity and beneficial species interactions that helped plants survive past stress episodes.
Led by University of Copenhagen, AEGIS will:
2024-2031
Carlsberg Research Laboratory, EMBL-EBI, Institut Pasteur, Seoul National University, University of Aarhus, University of Bremen, University of California, University of Cambridge, University of Colorado Boulder, University of Zurich, Wageningen, Wellcome Sanger Institute.
Ensembl Plants contains high-quality annotated reference genome assemblies for >100 model and crop species. Numerous plant genetic resources have been generated to capture and exploit genetic diversity, e.g. association mapping/diversity panels, many of which now come with founder genome assemblies and progeny variant datasets. However significant user bioinformatic, genetic and statistical expertise is required to analyse these genetic resources and interpret results in the context of the genes, genetic variants and appropriate reference genomes.
We will establish the 'Ensembl Plant Populations' platform - a web-tool containing existing population-based sequence and variant data, supporting users to run statistically sound genetic analyses. We focus on seven plant/crop species of relevance to UK researchers: wheat, barley, rice, brassica, arabidopsis, tomato and oat. The tool will provide an integrated pipeline to undertake genetic analyses from start to finish, including: (i) investigation of predicted power to detect genetic loci, (ii) adjustable forward genetic analysis settings, (iii) interactive genome-wide view of results, and (iv) presentation of useful information linked to genes and variants.
Improved access to plant genetic resources to drive crop innovation
2023-2026
Partner
A central focus of Wheat Alliance is to understand how wheat genetics influences the selection and maintenance of a beneficial root microbiome, particularly under nutrient-limited conditions that reflect real world farming constraints. To do this, the project will exploit the exceptional diversity of wheat germplasm available at Niab, including extensive novel genetic diversity introgressed from wheat’s close relatives into the restricted elite bread wheat gene pool.
This includes synthetic hexaploid wheats (SHW) and tetraploid wheat derived populations, generated by crossing wild emmer, emmer, and durum with modern winter and spring bread wheats to boost genetic diversity. Thousands of new wheat lines are available, including diverse multi-founder experimental populations, enabling systematic discovery of genetic factors that shape plant–microbe interactions and nutrient capture.
Using advanced phenotyping and data analytics, the project will link wheat genotype to root microbiome composition and function, and develop predictive approaches to identify the most effective plant–microbe combinations. Together, these outputs aim to support the development of wheat varieties and management strategies that maintain yields while reducing reliance on synthetic fertilisers.
Project team members at the annual meeting
New Research Aims To Boost Sustainable Wheat Nutrition Through Microbes
2024-2027
Facing Forwards aims to understand and exploit variation in epidermal features to future-proof cereal crops to changing climates.
To achieve this, we need to define the genes and developmental mechanisms controlling epidermal properties and how these affect plant performance.
Focusing on barley and wheat, the project explores the coordinating genetic network controlling epidermal traits linked to plant performance. These genes promote cuticular wax deposition as well as formation and spacing of specialised epidermal cells (such as stomata, epidermal hairs and silica cells) which help plants cope with stressful environments.
The project uses fine-scale cuticular profiling and single cell transcriptomics to reconstruct pathways leading to different cell types and cuticular chemistries, alongside mutant alleles in genes known to control specific features. Further, the project also explores the impact of altered epidermal patterning on leaf physiology and function - including stomatal conductance and intrinsic water use efficiency. These approaches will assess spatial and temporal control of epidermal patterning and the physiological impact of trait variation to identify desirable traits and ideotypes for crop production in future climates.
A summary of the genes/genetic loci investigated in the project, and their predicted effect on plant physiology. Source: Sarah McKim, University of Dundee.
2024-2027
Most of the modern apple varieties grown in the UK are susceptible to apple scab (caused by Venturia inaequalis), apple powdery mildew (caused by Podosphaera leucotricha) and European apple canker (caused by Neonectria ditissima). All three are fungal diseases which can cause serious yield and quality losses if not adequately controlled and their effective management is time consuming and significantly adds to the production costs. The long-term aim of the industry is to breed apples with resistance to these diseases, which will reduce production costs by avoiding the use of conventional spray control measures. However, breeding is a long-term process and typically takes 20-25 years from crossing to release.
The aim of this project is to develop novel breeding methodologies that will enable a shorter breeding cycle for apple and ensure a faster route to market for resistant varieties. The methodologies will include the use of genomic selection, marker assisted selection and speed breeding. These will be implemented in the Apple Breeding Consortium involving Niab and industry partner WorldWide Fruits Ltd.
Title: Next generation apple breeding for resilient UK production
Funder: Growing Kent & Medway
Industry partners: WorldWide Fruit Ltd
Term: June 2023 to March 2025
There are increasing numbers of privately funded breeding programmes in the UK soft fruit industry which would all benefit from a co-ordinated research approach to pre-breeding genetics of key traits and new breeding tools. This project is being funded by Defra to link academia to industry and develop our understanding of the genetics influencing improved tolerance to pests and diseases, and increased water and nutrient use efficiency in strawberry and raspberry. It will also develop genetic tools and resources for minor crops such as blackberry and honeyberry to support increased production in the UK.
Funder: Defra
Industry partners: ADAS and the James Hutton Institute
Term: October 2024 to June 2029
Funded by The Morley Agricultural Foundation (TMAF) and the JC Mann Trust, Niab is conducting multi-disciplinary research encompassing agronomy, genetics and molecular plant physiology to assess novel wheat genotypes in regenerative agriculture conditions.
Following a rotation based on winter wheat, trials will rotate across well-characterised experimental sites in East Anglia, with a known history of management. Fully replicated plot trials will evaluating the performance of new wheat genetic material (including resynthesised wheat (SHW) lines), under regenerative agricultural practices and lower nitrogen inputs.
The project ultimately aims to support growers and agronomists to produce high quantity and quality grains at low cost, and with limited environmental impact.
Niab is looking for farmers to share their experience of growing different wheat varieties in regenerative agriculture systems. Take our survey, so we can better understand which wheat varieties are widely cultivated and favoured by growers under these principles. Thank you for your support.
Poster: Novel wheat genotypes for regen-ag (2025)
September 2022 to August 2028
New Farming Systems research
Designing Future Wheat
This research project has now finished. The work is continued under the BBSRC-funded Designing Sustainable Wheat programme.
Wheat is a vital commercial crop and essential calorie source in the UK and globally. As the global population increases towards 10 billion people, with most increased consumption expected to occur in developing countries, the world will need to produce 60% more wheat by 2050 to meet global demand.
The BBSRC-funded Designing Future Wheat (DFW) programme was supported by eight UK research institutes and universities, including Niab, to develop the germplasm and techniques required by plant breeders to sustainably face these future production challenges. DFW continued the work started under the BBSRC-funded Wheat Improvement Strategic Programme (WISP) and consisted of four core work packages:
The DFW programme will develop improved germplasm for better yield, resistance to disease and a changing climate using high-throughput field technology and the genetic dissection of key traits. As part of this programme NIAB will be applying its extensive phenotyping expertise to maximise output from germplasm used within DFW, whether it be for drought tolerance or within hybrid wheat breeding programmes.
DFW aims to enhance grain quality for human health, combat diet-related diseases and improve the resilience of wheat to biotic stresses. As part of this programme NIAB is developing germplasm with starch characteristics that improve the processing ability and digestibility of wheat.
NIAB is characterising the novel genetic diversity captured from resynthesised wheat (SHW) and tetraploid wheats. This diversity is now in an elite wheat background and is available for exploration by the wheat research and breeding community. This is part of DFW’s target to accelerate the discovery and deployment of genes and alleles of high value for breeding, particularly from other parts of the DFW programme and previous BBSRC-funded research.
Large-scale genomic, phenotypic and regulatory datasets from other DFW work packages will be annotated, integrated and shared to generate critical reference resources supporting interpretation and driving new avenues of investigation.
Niab
Park Farm Campus
Villa Road
Histon
Cambridge
CB24 9AT, UK
Tel: +44(0)1223 342200
Email: [email protected]
