Assessing Illumina and Velvet for sequencing a wheat chromosome arm

World agriculture faces two major and unprecedented challenges in the near future. The first is to expand production of food and feed to meet increased demand while ensuring environmental sustainability. The second is to understand and mitigate the effects of global climate change on food and production. Wheat is one of the world's primary sources of food and feed and is the most important crop by scale and value in Europe. However, wheat yield gains seen in the past 20 years have not been maintained, mainly because germplasm improvement has not continued at sufficient pace to address the major challenges of sustainable food production and adapting to climate change. The new science of genomics can make major contributions to increasing both the scope and speed of crop improvement. But the complexity and size of the wheat genome are major obstacles to establishing biology, breeding and crop improvement strategies based on detailed knowledge of the complete genome sequence. Major advances in genome sequencing methods have led to the development of commercially available instruments that dramatically increase sequence output and reduce costs, and sequence analysis methods have been created to assemble and analyse the sequence generated. However, the strategies and methods required for applying this new technology to the wheat genome remain to be determined. In this proposal we aim to develop methods for sequencing the expressed regions of genes, large insert clones and purified chromosome arms using the Illumina sequencing platform, and to adapt the Velvet sequence assembly software to wheat genomics. The outputs of this project will facilitate the development of cost- effective and efficient strategies for sequencing the complete wheat genome when scaled up. The complete genome sequence of wheat will identify each gene in its correct location on the genomes and will determine the correct structures of genes. This knowledge will be a new foundation for biology projects that aim to understand the functions of wheat genes in processes such as disease resistance, environmental interactions, mineral nutrition and grain yield and nutrition. The methods we aim to develop will also be suitable for re-sequencing wheat lines, for example, commercial varieties that are used in breeding. By comparing these sequences to the reference genome and to each other scientists can identify sequence variation associated with traits. This information can be used to identify genes and lines with desirable genotypes of breeding populations. As such the technologies we aim to develop in this project will be the first step in advancing our capability to breed the next generations of our key crop plant.

Recent major advances in sequencing technology provide a timely opportunity to devise new sequencing strategies to tackle large and complex genomes that to date have been impracticable and unjustifiably expensive to sequence. We aim to assess the Illumina sequencing platform for generating transcriptome, BAC and genomic sequence of wheat, which has an extremely large (16 Gbp) hexaploid genome. The Illumina GA2 platform provides an excellent cost- effective sequence throughput that is continually being improved in terms of sequencing chemistry and base-calling. Although the GS-FLX Titanium system generates substantially longer read lengths, its cost per base is sufficiently higher than that of the Illumina platform to make the judgement that continued improvements in the Illumina platform will be adequate for generating sequence to sufficient depth for useful assembly of long contigs covering the low copy regions of wheat chromosomes. Once developed, these very cost- effective applications will be more readily taken up by the research community and applied for the rapid generation of wheat genome sequences. We also aim to develop specific computational and mathematical approaches to assemble and analyse wheat transcriptome and genome sequence. The outcomes of the proposed work will provide strategies for the cost effective sequencing of the complete wheat genome and for the compilation and analysis of the sequence into useful assemblies. Furthermore, strategies for targeting re-sequencing to gene-rich regions of the wheat genome will facilitate genotyping and association genetics studies in multiple commercial breeding lines.