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

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Genetics and Breeding

Abstract

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.

Technical Summary

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.

Planned Impact

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.

Publications

10 25 50
 
Description Article in Farmers Guardian 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Interview for an article published in Farmers Guardian "Genetic techniques will change varieties available by 2027" offering insights into the way in which research will shape the future of UK farming.
Year(s) Of Engagement Activity 2017
URL https://www.fginsight.com/news/news/genetic-techniques-will-change-varieties-available-by-2027-21106
 
Description Association of French Breeders workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact NIAB hosted Association of French Breeders workshop on wheat pre-breeding including talks, glasshouse and field demonstrations at NIAB Sophi Taylor (6/7/17). Increased international coordination on pre-breeding and shared examples of best practice and impact.
Year(s) Of Engagement Activity 2017
 
Description CIMMYT wheat breeding visit to NIAB 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact CIMMYT wheat breeding visit to NIAB: Alexey Morgounov and Tom Payne (16/6/17) including meeting and field visit to inspect breeding material in the field.
Year(s) Of Engagement Activity 2017
 
Description Interview for Arable Farming magazine 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Interview for comments/quotes published in 'Tools for a new plant breeding era', Andrew Blake, Arable Farming, June 2017 p26 - 27.
Year(s) Of Engagement Activity 2017
 
Description Invited seminar (Cranfield University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited seminar at Cranfield University "Technology-driven plant breeding" followed by Q&A and networking event.
Year(s) Of Engagement Activity 2017
 
Description Invited talk at Rothamsted Research Plant Sciences Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited talk at Rothamsted Plant Sciences Research Day "Technology-driven plant breeding" (13/7/17) covering research areas, findings and future directions
Year(s) Of Engagement Activity 2017
 
Description Key Note Speaker at VIII Argentinian Bioinformatics and Computational Biology Congress 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Key note speaker - meeting was followed by a number projects to apply for GCRF funding to work with researchers in Latin America
Year(s) Of Engagement Activity 2017
URL http://ufq.unq.edu.ar/8cab2c/
 
Description NIAB Open Day 2017 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact NIAB Open Day (27/6/17) including formal presentation of a seminar on the future of plant breeding innovation plus Q&A, tours of breeding material in the field and poster displays.
Year(s) Of Engagement Activity 2017
 
Description Visit of GRDC (Australia) to NIAB 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Supporters
Results and Impact Hosted visit of the Australian Grains Research and Development Corporation (GRDC) to NIAB (28/9/17) to explore partnering opportunities and to promote collaborations in crop breeding
Year(s) Of Engagement Activity 2017
 
Description Visit of KWS Biostatistics team 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Visit to NIAB of KWS Biostatistics team (based in Germany) 4 visitors to discuss statistical progress and collaborative opportunities (24/1/18)
Year(s) Of Engagement Activity 2018
 
Description Visit of Prof Ian Edwards (University of Western Australia) to NIAB 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Hosted visit of Prof Ian Edwards, University of Western Australia to NIAB to discuss collaborative NUE results and progress.
Year(s) Of Engagement Activity 2017