Award details

A wheat pan-genomics platform for enhanced genetic dissection of agronomic traits

Reference	BB/P010741/1
Principal Investigator / Supervisor	Dr James Cockram
Co-Investigators / Co-Supervisors	Professor Alison Bentley, Professor Mario Caccamo, Dr Keith Gardner
Institution	National Inst of Agricultural Botany
Department	Genetics and Breeding
Funding type	Research
Value (£)	379,288
Status	Completed
Type	Research Grant
Start date	01/07/2017
End date	30/11/2021
Duration	53 months

Abstract

This project integrates recent BBSRC-funded innovation in bread wheat genome re-sequencing/analysis capabilities at TGAC/JIC, with the 8-founder MAGIC population developed at NIAB, to address timely questions regarding the composition of the wheat 'pan-genome', and the ways in which this knowledge can be used for wheat genetic improvement. Specifically, this project will: -Produce and annotate high-quality reference sequences for the 8 MAGIC founders. -Produce and annotate high-quality reference sequences for two internationally important CIMMYT wheat lines. -Survey sequence of 94 maximally diverse wheat landraces from the Watkins collection to access a wide range of useful genetic variation. -Catalogue millions of sequence variants, including a systematic identification and characterisation of many types wheat structural variants, including chromosome rearrangements, CNV, PAV and InDels, in both genes and repeats. -Generate GbS data for 1,000 F9 MAGIC individuals, for identification of cross-over locations, haplotype characterisation, and construction of a POPSEQ genetic map for genome sequence scaffold anchoring and QTL analysis. -Via analysis of MAGIC phenotypic datasets (18 traits over 28 trials), delineate gene and genetic variant content within QTL intervals at unprecedented detail. -Characterise the effects of SV on genetic recombination rates and segregation distortion. -Deliver open-access MAGIC datasets, analysis tools, knowledge and training to the wheat R&D community and to industry. This project will deliver world-class knowledge, resources and training, and help maintain the UK's global position in wheat genetics and genomics, within a coordinated international framework.

Summary

Bread wheat (Triticum aestivum L.) is the UK's most important crop and the world's most widely cultivated cereal. Understanding the genetic make up of crops is essential for achieving increases in sustainable yield, disease resistance and adaptation to changing growing conditions. However this understanding has been lacking in wheat because it has a exceptionally complex genetic make-up. But recently BBSRC scientists have made a breakthrough in analysing the complete genetic make up of wheat. In this project we aim to build on the UK success by accessing the genetic make up of several key wheat varieties important for global agriculture, and to analyse this data to help identify useful genetic variation. This work will be carried out in an international framework that will maximise the benefit of UK research for this globally important crop.

Impact Summary

This project aims to develop resources and analytical tools for understanding and exploiting multiple wheat genome sequence assemblies. These have the potential to radically alter both wheat breeding and crop improvement, and also facilitate new areas of research that will lead to improved crops by understanding the contributions of genetic variation and gene function to traits. We aim to achieve the following objectives that will ensure that the proposed work achieves its maximal impact: To contribute to developing an international strategy for coordinating future work in wheat pan-genomics; To establish a network of collaborators and partners for applying outcomes of the research to genomics-led wheat improvement and promoting their uptake by breeders; To work with technology providers to develop new services and products to support genetic analyses of wheat based on multiple wheat genome assemblies; To demonstrate and promote the benefits of open access to technologies for generating wheat genomic assemblies, and genetic and genomic data; To train researchers from industry in the analysis and application of wheat genomics for breeding and technology development; To engage with the public about the excitement, power and societal impacts of genomics, enabling them to understand how it it applied for crop improvement, and to continue dialog about changes in how crops are produced. To encourage career development in plant science and genomics by hosting school visits and laboratory placements for school children. Impacts of International Coordination We will work with the Wheat Initiative to ensure this project achieves maximum synergies with related international activities, and that BBSRC achieves the best value for money and maximises its contributions to global wheat research. Impacts for plant breeders and biotechnology companies 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. We will continue in-depth engagement and training of crop breeders in new genomics technologies and quantitative genetic analysis approaches, and prioritise the development of new tools that will facilitate improved breeding. Breeders and other stakeholders will be invited to attend the three dedicated project workshops, during which we will highlight the availability of the project outputs for their own research and breeding. NIAB and JIC are regular contributors 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. Impacts for Growers and the Public We will engage with growers and the general public to establish a dialog about the potential impacts of genomics on crop production, how it might influence farming, consumers and the environment. Impacts for technology development companies and services We work with Illumina and other genomics companies to help develop technologies and services for cheaper, faster and better genetics and genomics analyses for large and complex crop genomes. Impacts for the crop R&D sector The size of this project and the disciplines involved, encompassing statistical/quantitative genetics, bioinformatics and genomics 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. TGAC, NIAB and JIC staff will benefit from exposure to complementary expertise in each other's institutes, encouraging further knowledge and skills exchange, and so helping to promote skills and opportunities within the research sector.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Crop Science, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/P010733/1 Wheat Pan-genomics

BB/P010768/1 Wheat Pan-Genomics

BB/P010768/2 Wheat Pan-Genomics

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