Low cost DNA identification of crop varieties

作物品种的低成本 DNA 鉴定

• 批准号: BB/T017031/1
• 负责人: Gary Barker
• 金额: $ 22.34万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FT017031%2F1
• 关键词: Low; cost; DNA; identification; crop

Wheat is the world's most widely grown commercial crop in terms of land area and yield and supplies 19% of all calories consumed. Global annual production is around 0.7 billion tonnes with a total export value of $46 billion. In the UK, wheat is the most important crop by yield at 15 million tonnes. Compared to other cereals, wheat lacks the genetic diversity required for resilience and yield increases in line with global demands. Unless germplasm diversity is managed with great care and coordination, selective breeding inevitably reduce diversity further over time. Efforts to direct elite variety crosses within the breeding industry and progress these rapidly to market are undermined by a complete lack of standardised varietal identification system, not just globally but even within the UK academic and breeding communities, leading to misidentifications within germplasm collections and a lack of interoperability between and among breeders, academics and regulators, all of whom use different genetic markers or none at all. In this proposal we will engage the international wheat community through the coordination umbrella of the Wheat Initiative, the UK breeding sector - via our partners at RAGT, and DSV and the regulatory framework of the British Society of Plant breeders to test and deploy an optimal set of genetic markers capable of discriminating wheat and other crop varieties at low cost. BBSRC funding over the past 20 years has brought us to the point where we have been able to screen thousands of hexaploid wheat lines with over 35,000 genetic markers. We have developed an algorithm that was able to select just 29 markers from these data that were able to discriminate all 2040 lines. In this project we will convert these markers to low cost KASP assays for use in industry and academia. The inclusion of the national and globally significant seed repository for wheat - the GRU at the John Innes Centre in addition to the majority of European breeding companies ensures that we can set the benchmark for genetic markers for wheat and lead by example globally. Our website, http://www.cerealsdb.uk.net which has been a key international repository for wheat genotyping data since 2004 will be used to disseminate the marker data and host a web tool for identifying varieties genotyped with our panel. The marker system will be made freely available and we anticipate primary impact through its widespread adoption as a standard system run in-house by breeders and academics. We will also offer this as a service at a total cost of £10 per sample (including DNA extraction) through our well-established Bristol Genomics Facility on a non-profit full economic cost basis.

就土地面积和产量而言，小麦是世界上种植最广泛的经济作物，并提供所有卡路里消耗的19%。全球年产量约为7亿吨，出口总额为460亿美元。在英国，小麦是最重要的作物，产量为1500万吨。与其他谷物相比，小麦缺乏适应性和产量增加所需的遗传多样性，以满足全球需求。除非对种质多样性进行非常谨慎和协调的管理，否则随着时间的推移，选择性育种不可避免地会进一步减少多样性。在育种行业内指导精英品种杂交并将其迅速推向市场的努力受到了完全缺乏标准化品种鉴定系统的破坏，不仅在全球范围内，甚至在英国学术界和育种界，导致种质收集中的错误鉴定以及育种者，学者和监管机构之间缺乏互操作性，所有这些人都使用不同的遗传标记或根本没有。在这项提案中，我们将通过小麦倡议的协调伞，英国育种部门-通过我们在RAGT和DSV的合作伙伴以及英国植物育种家协会的监管框架，参与国际小麦社区，以测试和部署一套最佳的遗传标记，能够以低成本区分小麦和其他作物品种。在过去20年中，BBSRC的资助使我们能够筛选出数千个具有超过35，000个遗传标记的六倍体小麦品系。我们开发了一种算法，能够从这些数据中选择29个标记，这些标记能够区分所有2040个品系。在这个项目中，我们将把这些标记物转化为低成本的KASP检测方法，用于工业和学术界。除了大多数欧洲育种公司之外，还包括国家和全球重要的小麦种子库-John Innes中心的GRU，确保我们可以为小麦遗传标记设定基准，并在全球范围内以身作则。自2004年以来，我们的网站http://www.cerealsdb.uk.net一直是小麦基因分型数据的主要国际存储库，将用于传播标记数据，并托管一个网络工具，用于识别与我们小组一起进行基因分型的品种。该标记系统将免费提供，我们预计通过广泛采用其作为育种者和学者内部运行的标准系统产生主要影响。我们还将通过我们完善的布里斯托基因组学设施提供这项服务，每个样本（包括DNA提取）的总成本为10英镑，以非营利的完全经济成本为基础。

项目成果

Detecting SARS-CoV-2 variants with SNP genotyping.

• DOI: 10.1371/journal.pone.0243185
• 发表时间: 2021
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Harper H;Burridge A;Winfield M;Finn A;Davidson A;Matthews D;Hutchings S;Vipond B;Jain N;COVID-19 Genomics UK (COG-UK) Consortium;Edwards K;Barker G
• 通讯作者: Barker G