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

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带注释的参考基因组汇编，可通过我们现有的Ensembl Plants平台进行基于网络的调查。同样，利用不同的方法捕获和利用遗传多样性，已经产生了许多植物遗传资源和种群。其中最重要的是作为植物研发的焦点社区资源，现在许多都带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、遗传变异和适当的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，它们的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进行协调整合，将使广泛的英国用户能够快速访问和使用这些补充数据集，用于多种植物物种。我们将建立“集成植物种群”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，允许用户使用关键的植物种群轻松地进行统计上合理的遗传分析。我们将重点关注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、拟南芥、番茄和燕麦。这些物种的选择是基于当前的英国用户访问统计数据，以及该物种对英国农业和研究的重要性。Ensembl植物种群工具将为用户提供从开始到结束进行遗传分析的集成管道，包括：(i)预先调查所选人群检测遗传位点的预测能力，（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程度的相关性，（iii）交互式全基因组视图的结果，允许用户移动到Ensembl Plants中确定的感兴趣的基因组位置。（iv）提供与已识别区域内的基因和变异相关的有用信息，以帮助用户确定候选基因以供进一步研究。我们将与英国植物研究界合作，选择合适的种群进行纳入，这一过程已经开始，并在整个项目期间参加社区会议，以提高认识并收集反馈，包括举办专门的利益相关者研讨会。通过为我们目前基于ensemble的工具、资源和用户基础增加目标价值，并将这些工具、资源和用户基础定制为对英国研究和农业高度重要的植物物种，我们的目标是最大限度地发挥这里产生的生物信息资源的影响。总的来说，这些活动将进一步支持更广泛的社区产生和基因分型的强大生物资源的利用和开发。

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.