Development and validation of a flexible genotyping platform for wheat

灵活的小麦基因分型平台的开发和验证

• 批准号: BB/I017496/1
• 负责人: Keith Edwards
• 金额: $ 22.15万
• 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: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI017496%2F1
• 关键词: Development; validation; flexible; genotyping; platform

Developing new strategies to manipulate yield and pest and disease resistance by marker-assisted selection (MAS) underpins the UK's strategy to generate improved wheat varieties. Academic laboratories, genotyping service providers and breeding companies use MAS to track the inheritance of a host of loci controlling desirable traits such as disease resistance, drought tolerance and yield. Until recently most laboratories have used microsatellite markers in their MAS projects, while these markers continue to be used, for many species Single Nucleotide Polymorphisms (SNPs) have become the marker of choice due to their ease of use and scoring and their ability to be automated with relative ease. However, in allohexaploid wheat the task of identifying similar useful sequence polymorphisms is problematical due to the occurrence of homoeologs from the A, B and D genomes. In this proposal, in collaboration, the John Innes Centre, IDna Genetics and KBioscience and Bristol University will develop both a wheat SNP database and a flexible genotyping platform for wheat. The utility of both will be validated by applying the tools and technologies to several exemplar projects. If successful users will be able to access the technology via two routes: The first consists of an in-house set-up requiring only basic molecular biology equipment (PCR machine and fluorescence plate reader). In this case, users would use the database to help them decide which assays to run and which primers/reagents (all publicly available through the database) to order and suggestions as to where these might be obtained. This constitutes a very low barrier for adoption as most users will be able to perform these SNP assays in house at the scale that best fits their purpose. This level of platform will be employed for the work carried out at JIC. The KASPar platform will replace JICs existing SSR genotyping service and, like the existing service, will be available for external work. An aliquot of the full set of KASPar primers will be kept at JIC and made available via this service. The second form of access consists of outsourcing to competitive service providers, such as KBioscience and IDna Genetics. Both companies have high-throughput platforms installed which will help lower costs and both will be set up to run all the KASPar assays developed in this project. The user would only need to provide genomic DNA and a list of which assays to run. In addition to KASPar, members of the community will be able to use the database to access a range of alternative genotyping technologies such as Illumina GoldernGate/Infinium/SureSelect, etc. For instance, the database will enable researcher to either design suitable probes for ordering from the appropriate technology supplier or they will be provided with details as to who offers the required technology on a commercial bases. This database will then be updated until at least 2017.

通过标记辅助选择（MAS）开发新的策略来控制产量和病虫害抗性，这是英国培育改良小麦品种战略的基础。学术实验室、基因分型服务提供商和育种公司使用MAS来跟踪控制诸如抗病性、耐旱性和产量等理想性状的大量基因座的遗传。直到最近，大多数实验室都在他们的MAS项目中使用微卫星标记，而这些标记继续被使用，对于许多物种来说，单核苷酸多态性（snp）由于其易于使用和评分以及相对容易自动化的能力而成为首选标记。然而，在异源六倍体小麦中，由于A、B和D基因组同源性的存在，鉴定相似的有用序列多态性的任务是有问题的。在该提案中，John Innes中心、IDna Genetics and KBioscience和Bristol大学将合作开发小麦SNP数据库和灵活的小麦基因分型平台。通过将工具和技术应用于几个范例项目，将验证两者的效用。如果成功，用户将能够通过两种途径获得这项技术：第一种是内部设置，只需要基本的分子生物学设备（PCR机和荧光板阅读器）。在这种情况下，用户将使用数据库来帮助他们决定运行哪些检测，以及订购哪些引物/试剂（所有这些都可以通过数据库公开获得），并建议从哪里获得这些引物/试剂。这构成了一个非常低的采用障碍，因为大多数用户将能够以最适合其目的的规模在内部执行这些SNP检测。这一级别的平台将用于JIC开展的工作。KASPar平台将取代JICs现有的SSR基因分型服务，与现有服务一样，将可用于外部工作。整套KASPar引物的一部分将保存在JIC，并通过该服务提供。第二种获取方式是将服务外包给有竞争力的服务提供商，如KBioscience和IDna Genetics。两家公司都安装了高通量平台，这将有助于降低成本，两家公司都将运行该项目中开发的所有KASPar分析。用户只需要提供基因组DNA和要运行的分析列表。除了KASPar，社区成员将能够使用该数据库访问一系列替代基因分型技术，如Illumina GoldernGate/Infinium/SureSelect等。例如，该数据库将使研究人员能够为向适当的技术供应商订货而设计适当的探针，或者向他们提供关于谁在商业基础上提供所需技术的详细资料。该数据库将至少更新到2017年。

项目成果

Additional file 1: of CerealsDB 3.0: expansion of resources and data integration

CerealsDB 3.0附加文件1：资源扩展与数据整合

• DOI: 10.6084/m9.figshare.c.3644624_d1
• 发表时间: 2016
• 作者: Wilkinson P

Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

• DOI: 10.1111/pbi.12183
• 发表时间: 2014-08
• 期刊: Plant biotechnology journal
• 影响因子: 13.8
• 作者: Wang S;Wong D;Forrest K;Allen A;Chao S;Huang BE;Maccaferri M;Salvi S;Milner SG;Cattivelli L;Mastrangelo AM;Whan A;Stephen S;Barker G;Wieseke R;Plieske J;International Wheat Genome Sequencing Consortium;Lillemo M;Mather D;Appels R;Dolferus R;Brown-Guedira G;Korol A;Akhunova AR;Feuillet C;Salse J;Morgante M;Pozniak C;Luo MC;Dvorak J;Morell M;Dubcovsky J;Ganal M;Tuberosa R;Lawley C;Mikoulitch I;Cavanagh C;Edwards KJ;Hayden M;Akhunov E
• 通讯作者: Akhunov E

CerealsDB 2.0: an integrated resource for plant breeders and scientists.

• DOI: 10.1186/1471-2105-13-219
• 发表时间: 2012-09-03
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Wilkinson PA;Winfield MO;Barker GL;Allen AM;Burridge A;Coghill JA;Edwards KJ
• 通讯作者: Edwards KJ

A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum.

种间变异转移到小麦中的步骤变化。

• DOI: 10.1111/pbi.12606
• 发表时间: 2017-02
• 期刊: Plant biotechnology journal
• 影响因子: 13.8
• 作者: King J;Grewal S;Yang CY;Hubbart S;Scholefield D;Ashling S;Edwards KJ;Allen AM;Burridge A;Bloor C;Davassi A;da Silva GJ;Chalmers K;King IP
• 通讯作者: King IP

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

• DOI: 10.1111/pbi.12485
• 发表时间: 2016-05
• 期刊: Plant biotechnology journal
• 影响因子: 13.8
• 作者: Winfield MO;Allen AM;Burridge AJ;Barker GL;Benbow HR;Wilkinson PA;Coghill J;Waterfall C;Davassi A;Scopes G;Pirani A;Webster T;Brew F;Bloor C;King J;West C;Griffiths S;King I;Bentley AR;Edwards KJ
• 通讯作者: Edwards KJ