Developing Next Generation Genetic Tools for Wheat

Lead Research Organisation: University of Liverpool
Department Name: Sch of Biological Sciences

Abstract

Food security is set to be one of the major challenges of the 21st century. By 2050, it is predicted that world food production will have to increased by 50%. This is against the pressures of global climate change and resource limitations. Meeting this challenge is going to require the development of innovative strategies which make use of our unprecedented knowledge of biology. Developing new, low input, high yielding varieties of wheat, will be fundamental to meeting these 2050 goals. The current world wheat harvest is approximately 650 million MT a year, making up a quarter of the world cereal harvest. Bread wheat is a hexaploid with a complex genome, five times the size of the human genome. At the University of Liverpool we are currently engaged in a project to decode the wheat genome using new 'next generation sequencing technology'. A sequenced genome for wheat, together with the development of new genetic tools exploiting this sequence data, will be key to meeting the increased food productivity goal. The aim of this proposal is a programme of retraining for me, built around developing the bioinformatics for two novel genetic analysis tools. The projects will make immediate use of the sequence data being generated at Liverpool. The first part of the project aims to develop a methodology to capture the gene-rich region of wheat. Using this capture technology, together with 'next generation sequencing technology' I will identify the region of the genome deleted in a dwarf line of wheat, rht12, and by identifying overlapping deletions the missing gene responsible for the dwarfing phenotype. Identifying the gene will allow us to understand the dwarfing mechanism in this variety. Dwarfism is a valuable economic trait and lay at the heart of the green revolution allowing increased nitrogen input without plants falling over. This deletion mapping strategy could be used to map other economical valuable deletion mutants. Wheat is made up of three genomes and the second part of the project is to develop a strategy to understand how these three genomes differentially respond to temperature. I will use 'next generation sequencing technology' adapting a technique call RNA-seq. Understanding how wheat responds to temperature at the molecular level will be important for mitigating the affect of global temperature increase on yield. Again , this new tool will be of considerable use to wheat researchers and other researchers working with crops with complex genomes. The proposal is in collaboration with researchers at Advance Genome Facility at the University of Liverpool and wheat geneticists at the John Innes Centre.

Technical Summary

Over the last 5 years there has been a radical change in the technologies used for sequencing DNA. The primary aim of this proposal is to retrain myself in the area of computational biology, allowing me to exploit the full potential of this technology in my existing research and develop a programme working closely at the interface of Arabidopsis and wheat research. Bread wheat is an allohexaploid with a genome size of 16GB. Wheat is one of the major world food crops and in 2007 the world wheat harvest was 605 million MT. It is predicted that by 2050 food production will have to have increased by 50%. This increase is against the pressures of competition for high quality agricultural land, resource limitations and adverse environmental conditions. Innovation and development of next generation genetic tools will be critical in meeting this goal. This retraining programme is built around developing the bioinformatics for two innovative approaches. The first approach, is to develop a wheat DNA capture array, based on the Nimblegen technology, secondly I will use the array and the SOLiD 3+ short read sequencing platform to map the rht12 deletion mutant in wheat. The deleted region will be identified primarily by the absence of homoeologous SNPs. The rht12 is a GA sensitive dwarf and understanding the mechanism of dwarfing in this line will have important economic value. The second innovation is to develop an RNA-seq approach for the analysis of the wheat transcriptome and differential regulation of homoeologous genes, again utilising the SOLiD3+. The approach will be used to investigate the response of the wheat transcriptome to temperature increases and how this response is altered in the ppd mutant. This mutation is incorporated globally into many wheat varieties.

Planned Impact

Next generation sequencing is set to have a huge impact on medicine and agriculture, this is recognised by industry. It is key to the competitiveness of UK research and industry that we increase the capacity of researchers capable of exploiting this technology. For agriculture specifically, these technologies must be exploited if we are to mitigate the effects of global temperature change and achieve the predicted increase in yield of 50% required by 2050, ensuring global food security. This proposal not only retrains me in this area, it also increases my understanding of wheat genetics and it develops two important tools for wheat geneticists and breeders utilising next-generation sequencing. Moreover, the pilot projects will identify the rht12 gene, a mutation of considerable economic potential and investigate the temperature responsiveness of the ppd mutant, a mutation used globally in wheat varieties. The technology developed in this project has obvious industrial applications. With Unilever, I have already established a mechanism of knowledge transfer (see letter of support) and have requested funds for this activity. The aim is for each year to make reciprocal visit between the two sites to explore how the new tools we are developing and generation sequencing can be exploited by Unilever in specific ongoing projects. I would aim to develop similar links with Nickersons, Syngenta and NIAB. I will also present this work at UK networking meetings and at International conferences. I will work with the University of Liverpool Business Gateway to help identify partners and further impact opportunities and with the recently formed, cross campus, Food Security Forum. I have also collaborated with Applied Biosystems, with both the Arabidopsis re-sequencing project (Ashelford et al. submitted) and an RNA-seq field trial. I will continue to develop this relationship, attending the annual European Solid Users Meetings. I will continue to develop this relationship and foster a similar relationship with Nimblegen, as a wheat genic enrichment array is likely to be of commercial interest. Engagement of the public in the BBSRC funded science I do is also important. To deliver this, I have developed a working relationship with the Liverpool World museum. For example in February, we will be involved in the 'Plantastic' exhibition, a £1 M project that will go on to tour Europe. In addition, I am also involved in the Nuffield Crest Award, taking sixth form students into my lab for a month each year to work on summer research projects (National Winners 2009). This project fulfils the aims of the BBSRC priority on 'Food Security', developing technology set to underpin future breeding programmes and investigating effect of temperature rises in a key UK crop, wheat. In addition, it delivers of the aims of the 'Technology Development for Bioscience' and 'Living with Environmental Change' priority areas.

Publications


10 25 50
Winfield MO (2012) Targeted re-sequencing of the allohexaploid wheat exome. in Plant biotechnology journal
 
Description My research development fellowship allowed me to re-skill in the area of computational biology. I achieved this through attend course at Cold Spring Harbour laboratories (CSHL), the University of Liverpool and Massachusetts Institute of Technology (MIT). Also through a series of projects trained in the bioinformatics associated with high-throughput sequencing technologies.

Work carried out during this fellowship, contributed to the generation of:
• The first sequence assemblies for the hexaploid wheat genome.
• An approaches for re-sequencing wheat which we have used to uncover diversity
• A rapid approach to mapping and uncovering the genes responsible for traits
• An approach for analyzing the wheat epigenome
Exploitation Route • We have generated a first draft wheat genome analysis, this is now underpinning international wheat research
• We have generated a wheat re-sequencing platform that has generated commercial wheat SNP (LGC) and has itself been commericalised by NimbleGen/Roche. These resources are now being used internationally
• We have used re-sequencing and a pseudo wheat genome to successfully map a mutant in wheat using a SHOREmapping approach. This approach can now rapidly be used to identify genes underlying traits
• We have developed an approach for characterising the wheat epigenome and identified genome specific differences in methylation state. This is now being used as pilot to uncover the full wheat epigenome and its function.
Sectors Agriculture, Food and Drink
 
Description We have developed an exome capture system that is now used by the global wheat community for resequencing wheat http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment/seqcap-ez-system/seqcap-ez-designs.html
First Year Of Impact 2014
Sector Agriculture, Food and Drink
Impact Types Economic
 
Description A computational cloud framework for the study of gene families
Amount £181,000 (GBP)
Funding ID BB/N023145/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2017 
End 09/2018
 
Description International Wheat Yield Partnership (IWYP).
Amount $2,000,000 (USD)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 01/2016 
End 01/2019
 
Title Method for mapping by sequencing in wheat 
Description I developing a wheat genic capture approach to re-sequencing wheat it was built in collaboration with an international consortium The Wheat Barley Exome Consortium is a collaboration of researchers from the University of Liverpool, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), James Hutton Institute, Kansas State University, University of Minnesota, University of Saskatchewan, and BIOGEMMA. 
Type Of Material Technology assay or reagent 
Year Produced 2011 
Provided To Others? Yes  
Impact This method has underpinned a large number of European and US grants to explore the genetic diversity of wheat. It has included 
URL http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment/seqcap-ez-system/seqcap-ez-d...
 
Description CIMMYT seeds of discovery 
Organisation Australian National University (ANU)
Country Australia, Commonwealth of 
Sector Academic/University 
PI Contribution Collaboration to provide Advance genetic approaches
Collaborator Contribution Access to wheat material and phenotyping data
Impact None yet
Start Year 2016
 
Description CIMMYT seeds of discovery 
Organisation CIMMYT
Country Mexico, United Mexican States 
Sector Charity/Non Profit 
PI Contribution Collaboration to provide Advance genetic approaches
Collaborator Contribution Access to wheat material and phenotyping data
Impact None yet
Start Year 2016
 
Description Combining field phenotyping and next generation genetics to uncover markers, genes and biology underlying drought tolerance in wheat. 
Organisation Indian Institute of Wheat and Barley Research
Country India, Republic of 
Sector Academic/University 
PI Contribution We are providing next generation genetic approaches to identity markers for Indian wheat
Collaborator Contribution Access to material and feild phenotyping
Impact Not yet
Start Year 2014
 
Description INvestigating TRiticeae EPIgenomes for Domestication 
Organisation Cold Spring Harbor Laboratory (CSHL)
Country United States of America 
Sector Charity/Non Profit 
PI Contribution Development of approaches to sequence the epigenome and bioinformatics pipelines
Collaborator Contribution access to material and expertise in systems genomic and bioinformatics.
Impact not yet
Start Year 2015
 
Description INvestigating TRiticeae EPIgenomes for Domestication 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Zentrum München
Country Germany, Federal Republic of 
Sector Public 
PI Contribution Development of approaches to sequence the epigenome and bioinformatics pipelines
Collaborator Contribution access to material and expertise in systems genomic and bioinformatics.
Impact not yet
Start Year 2015