The wheat Diverse MAGIC platform: Community Access to Resources, Protocols and Tools

Context
Wheat is the UK's most important crop, covering 1.6 million hectares and with an annual harvest worth £1.6 billion. Globally, demand for wheat is rising rapidly: it is estimated that by 2050, yield must rise by 60%. The best way to achieve gains in the key wheat breeding targets is to develop improved varieties. The ongoing revolution in genetic and molecular tools for wheat breeding is poised to deliver step changes in wheat genetic gain. However, comparatively little investment has been focused on the development of suitable biological resources to best take advantage of these tools.
This project builds on previous publicly-funded investment in a state-of-the-art wheat biological platform: the Multiparent Advanced Generation Inter-Cross (MAGIC) population (termed, 'Diverse MAGIC'). Created over four years by inter-crossing 16 UK wheat varieties over multiple generations, the resulting population of over 600 lines represents a unique resource within the UK and worldwide. By capturing large amounts of genetic variation (from the 16 parents) and efficiently reshuffling these over multiple generations of crossing, the population is well placed to serve as a central resource for a broad spectrum of the UK wheat bioscience community.

Aims and objectives
This project brings together expertise from the plant and animal MAGIC sectors, to develop Diverse MAGIC into an integrated community platform for wheat genetics and breeding. This will be achieved by developing Diverse MAGIC resources, tools and community engagement programs that will enable effective use of Diverse MAGIC within the UK community. Specifically, it will:
1) Enlarge the Diverse MAGIC population to 800 lines.
2) Provide access to Diverse MAGIC seed.
3) Establish a catalogue of genetic and phenotypic variation present in the 16 MAGIC parents.
4) Provide baseline field phenotype and high-density genotype data on the whole population.
5) Develop bioinformatic and software tools tailored to wheat MAGIC.
6) Provide dissemination and training events to promote uptake of MAGIC in wheat.
7) Establish and promote Diverse MAGIC 'community phenotyping' events.
8) Collate the wheat MAGIC resources generated, and make freely accessible via the project website.

Applications and benefits
The biological and supporting resources generated by this project will stimulate new research, amplify output from existing wheat programs, and aid the translation of scientific discoveries to breeders, farmers and processors. The Diverse MAGIC resource complements existing UK wheat resources for gene validation, and will help promote collaborative research within the crop genetics sector.

Multi-parent Advanced Generation Inter-Cross (MAGIC) populations represent a new generation of plant mapping resources ideally suited to community-based crop improvement. This project is based around a new wheat population recently completed at NIAB with BBSRC funding: the 16 parent Diverse MAGIC population. Using the expertise in plant and animal multi-parent populations developed at NIAB and WTCHG, this project will build germplasm, analytical and database resources around Diverse MAGIC, transforming it into a complete community resource for wheat R&D.
1) Biological resource utilization
The Diverse MAGIC population will be consolidated, and germplasm made available for public access. Phenotypic data on the parents and population will be generated using traditional and precision phenomics approaches, providing baseline datasets to pump-prime community engagement. Field trials will also serve as a community phenotyping resource, allowing third parties to collect additional phenotypic data. Dissemination and training will be provided at MAGIC workshops, in which Diverse MAGIC datasets will be used to demonstrate the analytical software and resources developed at WTCHG.
2) Wheat analysis tools
WTCHG will develop a suite of tools and software for wheat MAGIC, based around those they previously developed for Arabidopsis MAGIC. A catalogue of genetic variants between the 16 founders will be developed, the population genotyped with a high-density genetic marker array, and a high-resolution genetic map constructed. The software HAPPY will be adapted to construct genome mosaics for the Diverse MAGIC population, and software adapted to perform QTL mapping in wheat. All project resources will be made freely accessible via the project website and associated database.

The immediate beneficiaries of this project will be academic and commercial groups working on the development of new varieties of wheat for use by UK agriculture. This follows from the fact that the 16 founders of the Diverse MAGIC population capture much of the genetic variation segregating in wheat varieties commonly grown in the UK. Use of the Diverse MAGIC population will help identify genetic loci containing variation that affect traits of UK agronomic importance for selection within the UK genepool. This will have a long-term beneficial impact on UK food security and the sustainable intensification of agriculture. A notable feature of the population is that it includes older UK varieties in addition to modern accessions. This means that it can detect QTL segregating between these two groups, potentially identifying favourable alleles which have been "left behind." This is not practical in association mapping panels since population structure is confounded with variety age.

Commercial wheat breeders will benefit by:
1) Markers diagnostic for linkage between individual genes or small genetic intervals and components of the traits measured on the population.
2) Release of all trait and marker data, which can be combined with their own from this and other populations.
3) Protocols and software for their own analyses in MAGIC
4) Release of seed. The MAGIC lines will be highly recombined and may have novel combinations of QTL. These lines are candidates for further assessment and for crossing.

Breeders and other stakeholders will be invited to view plots at events during which we will inform the community of the availability of these resources for their own research and breeding. NIAB is a regular contributor to events such as CEREALS: the leading technical event for the UK arable industry. We will ensure that the project is represented there and will attend in person to disseminate information.

MAGIC populations have been created or are being created for other crops and in other countries. The development of statistical and computational methods in this project will be of direct use for marker and trait mapping in these other populations. We are already in contact with the researchers and breeders involved in many of these populations. We will build on these contacts informally, through correspondence and visits, and also through the workshops organised within this project.

NIAB / WTCHG staff will benefit from exposure to complementary expertise in each other's institutes. For NIAB this will result in improved application of big-data methods to their research interests in agricultural science and genetics. For WTCHG, it will open opportunities for broader application of its statistical genetics research in agriculture and for future funding and collaboration with plant science communities.

The size of this project and the disciplines involved, encompassing statistical/quantitative genetics, molecular genetics and agronomy will provide opportunities for training of scientific and technical staff in these fields. This will occur on an ad-hoc basis and through the scheduled training courses and workshops.