Nanopore technologies for Septoria Surveillance

用于壳针孢监控的纳米孔技术

• 批准号: BB/N021886/1
• 负责人: Mario Caccamo
• 金额: $ 19.91万
• 依托单位: National Institute of Agricultural Botany
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN021886%2F1
• 关键词: Nanopore; technologies; Septoria; Surveillance

Septoria tritici blotch (STB) of wheat is the most economically important disease affecting wheat production in Northern Europe. STB is controlled using a combination of agronomy, genetic resistance and fungicides however, selection and subsequent adaptation of the underlying pathogen populations can lead to breakdowns in host resistance and resistance to chemical controls. As the pathogen adapts we will need to understand the composition of the pest population (or pathotypes) to be able to describe specific differences between members of the same species and how these differences affect the range of wheat varieties affected by STB. An effective and cost-efficient solution for STB will directly depend on our understanding of the underlying pathogen (Zymoseptoria tritici). The use of advanced sequencing technologies has the potential to quickly and efficiently screen many individual pathogen isolates, providing a wealth of information at a low cost. This type of approach has already been demonstrated to be a powerful tool in yellow rust of wheat. However, the cost of purchasing machinery required to conduct sequencing is often prohibitive and runs can take between 24-48 hours to complete. There are also requirements for high-powered computing facilities and experienced operators to conduct the relevant analyses to arrange sequencing data in to a practical format. NanoPath will employ the MinION sequencer from Oxford Nanopore Technologies as a surveillance tool to improve the speed and ease at which researchers can identify and survey new pests in the field. This will first assess the utility of the MinION and help to develop a model and computational platform to apply nanopore sequencing to a wider range of crop pathogens. The MinION device is portable and able to generate sequencing data following a relatively easy-to-use process. We also propose to implement a data analysis pipeline that will make use of a number of open-source primary data software tools optimised for the discovery and characterisation of genetic variants this crop pathogen.

小麦壳针孢斑点病（STB）是影响北方小麦生产的重要病害。STB使用农艺学、遗传抗性和杀真菌剂的组合来控制，然而，潜在病原体群体的选择和随后的适应可导致宿主抗性和对化学控制的抗性的破坏。随着病原体的适应，我们需要了解害虫种群（或致病型）的组成，以便能够描述同一物种成员之间的具体差异，以及这些差异如何影响受STB影响的小麦品种的范围。STB的有效和具有成本效益的解决方案将直接取决于我们对潜在病原体（Zymoseptoria trivulae）的了解。使用先进的测序技术有可能快速有效地筛选许多单个病原体分离株，以低成本提供丰富的信息。这种类型的方法已经被证明是一个强大的工具，在小麦黄锈病。然而，购买进行测序所需的机器的成本通常令人望而却步，并且运行可能需要24-48小时才能完成。还需要高性能的计算设施和经验丰富的操作员进行相关分析，以将测序数据整理成实用的格式。NanoPath将采用牛津纳米孔技术公司的MinION测序仪作为监测工具，以提高研究人员识别和调查该领域新害虫的速度和便利性。这将首先评估MinION的实用性，并帮助开发一个模型和计算平台，将纳米孔测序应用于更广泛的作物病原体。MinION设备是便携式的，并且能够在相对易于使用的过程之后生成测序数据。我们还建议实施一个数据分析管道，该管道将利用许多开源原始数据软件工具，这些工具针对发现和表征这种作物病原体的遗传变异进行了优化。

项目成果

(Article) Applying new technology to pathogen surveillance

（文章）新技术应用于病原体监测

• 期刊: NIAB Landmark Magazine - Quarterly publication distributed to network membership (>700 subscriptions)
• 作者: Wood T A