Assessing Illumina and Velvet for sequencing and assembling a wheat chromosome arm.

评估 Illumina 和 Velvet 对小麦染色体臂的测序和组装。

• 批准号: BB/G024650/1
• 负责人: Michael Bevan
• 金额: $ 9.13万
• 依托单位: John Innes Centre
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG024650%2F1
• 关键词: Assessing; Illumina; Velvet; sequencing; assembling

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.

在不久的将来，世界农业面临两大前所未有的挑战。第一是扩大粮食和饲料的生产，以满足日益增长的需求，同时确保环境的可持续性。二是了解和减轻全球气候变化对粮食和生产的影响。小麦是世界粮食和饲料的主要来源之一，是欧洲规模和价值最重要的作物。然而，过去20年来小麦产量的增加并没有得到保持，主要是因为种质改良没有继续以足够的速度应对可持续粮食生产和适应气候变化的重大挑战。基因组学这门新科学可以为提高作物改良的范围和速度做出重大贡献。但是小麦基因组的复杂性和大小是建立基于完整基因组序列的详细知识的生物学、育种和作物改良策略的主要障碍。基因组测序方法的重大进展已经导致了商业上可获得的仪器的发展，其显著增加了序列输出并降低了成本，并且已经创建了序列分析方法来组装和分析所产生的序列。然而，将这项新技术应用于小麦基因组所需的策略和方法仍有待确定。在这项提案中，我们的目标是开发使用Illumina测序平台对基因的表达区域、大插入克隆和纯化的染色体臂进行测序的方法，并使Velvet序列组装软件适应小麦基因组学。这一项目的成果将有助于制定成本效益高和效率高的战略，以便在扩大规模时对小麦全基因组进行测序。小麦的完整基因组序列将确定每个基因在基因组上的正确位置，并确定基因的正确结构。这些知识将为生物学项目奠定新的基础，这些项目旨在了解小麦基因在抗病性，环境相互作用，矿物质营养以及谷物产量和营养等过程中的功能。我们旨在开发的方法也将适用于重新测序小麦品系，例如用于育种的商业品种。通过将这些序列与参考基因组进行比较，科学家们可以确定与性状相关的序列变异。这些信息可用于鉴定育种群体中具有理想基因型的基因和品系。因此，我们在这个项目中开发的技术将是提高我们培育下一代关键作物能力的第一步。

项目成果

Analysis of the bread wheat genome using whole-genome shotgun sequencing.

使用全基因组shot弹枪测序分析面包小麦基因组。

• DOI: 10.1038/nature11650
• 发表时间: 2012-11-29
• 期刊: Nature
• 影响因子: 64.8