Can we produce a better wheat crop to feed the world? Single to multiple wheat genomics
12 January 2017
Entering a ‘wheat pan-genomics’ era from single to multiple wheat DNA references, the Earlham Institute (EI) aims to diversify one of the world’s most complex genomes to improve yield quality and increase wider production of this critical food crop.
Bread wheat (Triticum aestivum L.) is the UK's most economically important crop and the world's most widely cultivated cereal. Wheat production is vital in both emerging and growing economies. Therefore, understanding the genomics of wheat is essential to sustain increased yields for the growing global population, while protecting the crop from common disease epidemics and adaptation to extreme climate change conditions.
The wheat genome has been an enigma to scientists due to its exceptionally large and complex genome. Previously leading a first complete analysis of the bread wheat genome with other BBSRC-funded institutes, EI
From the most sourced plant data reference1 released in November 2015, EI
The new wheat analyses came to fruition after delivery of the first wheat reference using the bioinformatics ‘w2rap’ tool for genome assembly developed by Bernardo Clavijo and his Algorithm Development Team at EI. Life science industry leaders Bayer Crop Sciences approached the team to run a pilot project sequencing a commercially significant wheat variety.
Now, the industry-academia partnership has resulted in a further four varieties being commissioned. A relationship that gives the industry access to unprecedented genome analysis power, while supporting the development of EI’s wheat genomics methods.
W2rap is a bioinformatics pipeline that can decipher complex genomes and produce robust assemblies to guide precision breeding. This genome assembly method will be applied to EI’s further wheat analysis, using tailored data generation based on work of the Institute’s Platforms and Pipelines Group at EI.
The unique tool will not only be able to assemble the wheat varieties sequence data but allow wheat genomes to be produced effectively, robustly and efficiently with next-generation sequencing technologies.
In parallel to this, a £2m grant funded by BBSRC to EI in collaboration with the John Innes Centre (JIC) and NIAB, led by Dr Matt Clark, will aim to understand the genetic makeup of 14 different varieties of wheat cultivars important for global agriculture and analyse this data to help map the genetic variation in the crop. This project includes the further sequencing and assembly of eight more wheat lines with the w2rap
Prof Neil Hall, Director of EI, said: “These new projects are extremely timely as technical advances we have made in assembly and analysis of the wheat genome have overcome the hurdles in complexity and now enable us to approach wheat genetics in a whole new way. Now we should see the rapid advances in breeding programs that have previously been possible in other crops.”
Fred Van Ex, Head of the Genomics group at Bayer Crop Science, said: “More than two billion people worldwide rely on wheat as a staple food. In order to meet demands of the growing world population, Bayer is dedicated to
Bernardo Clavijo, Bioinformatics Algorithms Project Leader, said: “w2rap will be of great value for public wheat initiatives; helping us to advance into wheat pan-genomics
“In terms of global food security, the gains are twofold. The immediate incorporation of new technology into the breeding programme allows breeders to produce better varieties faster and cheaper. As well as the methods we develop enabling a fast transition from a
Grant lead Dr Matt Clark, Head of Technology Development at EI, said: “These new wheat genomes sequences have the potential to radically alter both wheat breeding and crop improvement. Facilitating new areas of research in understanding the contributions of genetic variation and gene function to the crop’s many different traits.
“Working within an international strategic framework, the project will maximise the benefit to UK research and industry wheat breeding practices. Delivering world-class knowledge, resources and training to help maintain the UK's global position in wheat genomics and contributing to the priority of global food security.”
Notes to editors
1) Ensembl Plants – the genome annotation system is developed jointly by the EBI and the Wellcome Trust Sanger Institute, which is used for the annotation, analysis and display of genomes, including plants and vertebrates.
2) Accompanying images can be accessed, here. Images show wheat variety products. For 'USDA wheat' image, credit: Keith Weller, USDA.
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The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £6.45M in 2015/2016 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.
The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.