UK Crop Diversity Bioinformatics Resource

英国作物多样性生物信息学资源

基本信息

批准号：
BB/S019669/1
负责人：
Mario Caccamo
金额：
$ 75.85万
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：
2019
资助国家：
英国
起止时间：
2019 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FS019669%2F1
关键词：
UK Crop Diversity Bioinformatics Resource

项目摘要

We are requesting a High-Performance Computing (HPC) cluster that will be dedicated to support and expand the work that of a consortium of six leading UK research organisations with a focus on the characterisation and utilisation of novel genetic diversity for both the improvement of current crops as well as the breeding of novel varieties. The platform will be open to researchers at the participating institutions and their extensive network of collaborators. We will also develop and deploy common genomics workflows relevant to the common interests of the partners in crop diversity informatics. Developments in sequencing and genotyping technologies together with advances in environmental monitoring and characterisation are leading to rapid changes in the opportunities that are available to evaluate and utilise genetic diversity in crop plants and their wild relatives to adapt to the changing landscape of agriculture. This is driven by the increasing impact of climate change as well as by evolving agricultural practices and commodity demand. UK Research Organisations host a wide range of key expertise and information resources that have the potential to play a critical role in ensuring that this potential is fully realised. A major factor in developing the research infrastructure to support and nurture such activities is the provision of access to suitable computational resources that are tailored to the key data resources and analytical tools that that play a central role. A consortium of UK Research Organisations including NIAB, Royal Botanic Gardens, Kew (RBGKew), the Natural History Museum (NHM), the James Hutton Institute (JHI), Royal Botanic Gardens, Edinburgh (RBGE), and Scotland's Rural College (SRUC) have identified a need for additional computing resources beyond what they already host individually, centred on BBSRC-funded work around crop diversity. An high-performance computing (HPC) resource focused on the common needs of our organisations and tailored to the software and data resources which are relevant to this mission will deliver efficiencies in the use of resources, both in terms of computing hardware and systems administration. In addition, it will act as a focus for sharing data, developing new methods of analysis and delivering training, and a platform for developing new collaborative programmes of innovative science. Within the partner organisations alone, the platform will support the work of more than 400 scientists including a large proportion of early career researchers and PhD students. We propose to host the facility at JHI's data centre.

我们要求一个高性能计算（HPC）集群，该集群将致力于支持和扩展六个英国领先研究组织的财团的工作，重点是对新型遗传多样性的特征和利用，以改善当前农作物的改善以及新型品种的繁殖。该平台将向参与机构及其广泛合作者网络的研究人员开放。我们还将开发和部署与合作伙伴在作物多样性信息学方面的共同利益相关的共同基因组学工作流。测序和基因分型技术的发展以及环境监测和表征方面的进步导致了机会的迅速变化，这些机会可用于评估和利用作物植物及其野生亲戚的遗传多样性，以适应不断变化的农业景观。这是由于气候变化以及不断发展的农业实践和商品需求的不断增加的影响所致。英国研究组织拥有广泛的关键专业知识和信息资源，有可能在确保完全实现这一潜力的情况下发挥关键作用。开发研究基础架构以支持和培养这种活动的主要因素是提供适合针对起着核心作用的关键数据资源和分析工具量身定制的合适计算资源。英国研究组织的联盟，包括NIAB，皇家植物园，库维（RBGKew），自然历史博物馆（NHM），詹姆斯·赫顿研究所（JHI），皇家植物园，爱丁堡（RBGE）（RBGE）和苏格兰乡村学院（SRUC），他们已经在围绕着其他范围的人进行了训练，他们已经确定了一些人，他们已经确定了一些人，他们已经确定了一些人，他们已经在范围内进行了一些委托，他们已经在围绕着其他人进行了训练。多样性。高性能计算（HPC）资源的重点是我们组织的共同需求，并针对与此任务相关的软件和数据资源量身定制，这将在计算硬件和系统管理方面提供资源使用的效率。此外，它将成为共享数据，开发新的分析和提供培训方法的重点，以及开发创新科学新协作计划的平台。仅在合作伙伴组织中，该平台将支持400多名科学家的工作，其中包括很大一部分职业研究人员和博士生。我们建议将该设施托管在JHI的数据中心。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila pseudoobscura.

DOI：
10.1093/gbe/evad113
发表时间：
2023-07-03
期刊：
GENOME BIOLOGY AND EVOLUTION
影响因子：
3.3
作者：
Barata, Carolina;Snook, Rhonda R.;Ritchie, Michael G.;Kosiol, Carolin
通讯作者：
Kosiol, Carolin

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

HISS：基于 Snakemake 的工作流程，用于执行 SMRT-RenSeq 组装、AgRenSeq 和 dRenSeq，用于发现新型植物抗病基因

DOI：
10.1101/2022.11.01.514708
发表时间：
2022
期刊：
影响因子：
0
作者：
Adams T
通讯作者：
Adams T

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula.

DOI：
10.3390/plants10050946
发表时间：
2021-05-10
期刊：
Plants (Basel, Switzerland)
影响因子：
0
作者：
Carballo J;Zappacosta D;Marconi G;Gallardo J;Di Marsico M;Gallo CA;Caccamo M;Albertini E;Echenique V
通讯作者：
Echenique V

Eragrostis curvula, a Model Species for Diplosporous Apomixis.

DOI：
10.3390/plants10091818
发表时间：
2021-08-31
期刊：
Plants (Basel, Switzerland)
影响因子：
0
作者：
Carballo J;Zappacosta D;Selva JP;Caccamo M;Echenique V
通讯作者：
Echenique V

The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.

DOI：
10.1111/tpj.15908
发表时间：
2022-09
期刊：
PLANT JOURNAL
影响因子：
7.2
作者：
Chen, Yun-Yu;Schreiber, Miriam;Bayer, Micha M.;Dawson, Ian K.;Hedley, Peter E.;Lei, Li;Akhunova, Alina;Liu, Chaochih;Smith, Kevin P.;Fay, Justin C.;Muehlbauer, Gary J.;Steffenson, Brian J.;Morrell, Peter L.;Waugh, Robbie;Russell, Joanne R.
通讯作者：
Russell, Joanne R.