Ensembl plant populations: integrating trait analyses and population-based sequence variants into a browsable genomic context

Ensembl 植物种群：将性状分析和基于种群的序列变异整合到可浏览的基因组环境中

• 批准号: BB/X018695/1
• 负责人: Sarah Dyer
• 金额: $ 62.28万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX018695%2F1
• 关键词: Ensembl; plant; populations; integrating; trait

The plant R&D community has generated high-quality annotated reference genome assemblies for numerous model and crop species, available for web-based investigation via our existing Ensembl Plants platform. Similarly, numerous plant genetic resources and populations have been generated using different approaches to capture and exploit genetic diversity. The most important of these serve as focal community resources for plant R&D, and many now come with associated parental genome assemblies and extensive variant data on the offspring. However, making use of these genetic resources and analysing the results in the context of the genes, genetic variants and appropriate reference genomes, remains a disjointed workflow and their use requires significant bioinformatic, genetic, statistical and technical expertise from users. Coordinated integration of the results of genetic analyses with variant datasets against one or more reference genomes within the familiar Ensembl Plants environment would enable a broad range of UK users to rapidly access and use these complementary datasets for multiple plant species. We will establish the 'Ensembl Plant Populations' platform - a web-tool containing existing population-based sequence and variant data, allowing users to easily run statistically sound genetic analyses using key plant populations. We will focus on seven plant/crop species of high relevance to UK researchers: wheat, barley, rice, brassica, arabidopsis, tomato and oat. These species have been selected based on current Ensembl Plants UK user access statistics, and on the importance of the species to UK agriculture and research. The Ensembl Plant populations tool will provide users with an integrated pipeline to undertake genetic analyses from start to finish, including: (i) upfront investigation of the predicted power of the selected population to detect genetic loci, (ii) inclusion of pre-prepared statistics to support users e.g. to account for varying levels of relatedness between genotypes, (iii) interactive genome-wide view of the results allowing users to move to identified genomic locations of interest in Ensembl Plants, (iv) presentation of useful information linked to genes and variants within those identified regions to help users identify candidate genes for further study. We will work with the UK plant research community to select appropriate populations for inclusion, a process which has already started, and attend community meetings throughout the project to raise awareness and gather feedback, including holding a dedicated stakeholder workshop. By adding targeted value to our current Ensembl-based tools, resources, and user-base, and tailoring these to plant species of high importance to UK research and agriculture, we aim to maximise the impact of the bioinformatic resources generated here. Collectively, these activities will further support the use and exploitation of the powerful biological resources the wider community has generated and genotyped.

植物研发社区已经为许多模型和作物物种生成了高质量的注释参考基因组组装，可通过我们现有的Ensembl Plants平台进行基于网络的调查。同样，许多植物遗传资源和种群也是利用不同方法获取和利用遗传多样性而产生的。其中最重要的是作为植物研发的焦点社区资源，许多现在都有相关的亲本基因组组装和后代的广泛变异数据。然而，利用这些遗传资源并在基因、遗传变异和适当参考基因组的背景下分析结果，仍然是一个脱节的工作流程，其使用需要用户提供大量的生物信息学、遗传学、统计学和技术专门知识。在熟悉的Ensembl Plants环境中，将遗传分析结果与针对一个或多个参考基因组的变异数据集协调整合，将使广泛的英国用户能够快速访问和使用多个植物物种的这些互补数据集。 我们将建立“Ensembl Plant Populations”平台-一个包含现有基于种群的序列和变异数据的网络工具，允许用户使用关键植物种群轻松进行统计上合理的遗传分析。我们将专注于与英国研究人员高度相关的七种植物/作物物种：小麦，大麦，水稻，芸苔属，拟南芥，番茄和燕麦。这些物种是根据目前Ensembl Plants UK用户访问统计数据以及该物种对英国农业和研究的重要性选择的。Ensembl植物种群工具将为用户提供一个完整的管道，从开始到结束进行遗传分析，包括：（i）预先调查选定群体检测遗传基因座的预测能力，（ii）包括预先准备的统计数据以支持用户，例如考虑基因型之间不同水平的相关性，（iii）结果的交互式全基因组视图，允许用户移动到Ensembl Plants中感兴趣的已识别基因组位置，（iv）呈现与这些已识别区域内的基因和变体相关的有用信息，以帮助用户识别候选基因以进行进一步研究。我们将与英国植物研究界合作，选择合适的群体进行纳入，这一过程已经开始，并在整个项目期间参加社区会议，以提高认识和收集反馈，包括举办专门的利益相关者研讨会。通过增加有针对性的价值，我们目前的合奏为基础的工具，资源和用户群，并定制这些高度重要的植物物种，英国的研究和农业，我们的目标是最大限度地发挥生物信息资源的影响在这里产生。总的来说，这些活动将进一步支持使用和开发更广泛的社区产生的强大生物资源和基因分型。