Big Data Infrastructure for Crop Genomics

作物基因组学大数据基础设施

• 批准号: BB/M018458/1
• 负责人: Sarah Dyer
• 金额: $ 255.12万
• 依托单位: Earlham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM018458%2F1
• 关键词: Big; Data; Infrastructure; Crop; Genomics

Recent advances in sequencing technologies and computational tools have made it possible to sequence the genomes of some of the world's most important crop species, such as rice, barley, rapeseed, maize, soya and wheat. These crops constitute a substantial part of the daily food intake for most of the population of the world and any improvements in the breeding for more efficient and nutritious varieties will have a direct impact on ensuring global food security. Whilst obtaining the genome sequences for these crops provides a hugely useful resource for giving insights into the differences between species, it is through sequencing different individuals from the same or closely-related species which allows us to identify useful genetic variants which can be selected for during plant breeding. These approaches require a combination of sequence and phenotypic data, plus analysis tools. We propose to develop a crop bioinformatics platform which enables users to access this genetic and phenotypic variation and perform analyses to explore gene expression and associations between genetic variation and traits. The platform will be developed using open source principles and publicly available data. Population-wide genetic variants will be represented on a genomic data structure; an archiving system for storing plant phenotype data will be developed; tools to allow the querying of these datasets and analyses to link genotype to phenotype will be implemented; and the platform will be accessible via TGAC and EBI servers but also packaged into a virtual machine for easy installation on users' local hardware. This novel platform for crop bioinformatics will promote opportunities for collaborative work with R&D groups in industry, research and academia. The availability of data generated by publicly funded resources, and the concomitant development of new, production-quality tools will lower the barriers to information-enabled crop science, stimulating new opportunities for research and application. The platform will also open up new opportunities for the UK bioinformatics community, traditionally focused on biomedical applications, by developing alternative career paths around biotechnology and agri-food.

测序技术和计算工具的最新进展使测序世界上一些最重要的作物物种的基因组成为可能，如水稻、大麦、油菜籽、玉米、大豆和小麦。这些作物构成了世界上大多数人口每日食物摄入量的很大一部分，在培育更高效和更有营养的品种方面的任何改进都将对确保全球粮食安全产生直接影响。虽然获得这些作物的基因组序列为洞察物种之间的差异提供了非常有用的资源，但通过对相同或密切相关物种的不同个体进行测序，使我们能够识别有用的遗传变异，这些变异可以在植物育种中进行选择。这些方法需要序列和表型数据的组合，以及分析工具。我们建议开发一个作物生物信息学平台，使用户能够访问这种遗传和表型变异，并进行分析，以探索基因表达和遗传变异与性状之间的关联。该平台将使用开放源码原则和公开可用的数据进行开发。将在基因组数据结构中显示整个种群的遗传变异；将开发用于存储植物表型数据的存档系统；将使用工具来查询这些数据集和分析，以便将基因型与表型联系起来；该平台将可通过TGAC和EBI服务器访问，但也将被打包到一个虚拟机中，以便于安装在用户的本地硬件上。这个新的作物生物信息学平台将促进与工业、研究和学术界的研发小组合作的机会。由公共资助的资源产生的数据的可用性，以及随之而来的新的、生产质量的工具的开发，将降低实现信息驱动的作物科学的壁垒，刺激新的研究和应用机会。该平台还将通过围绕生物技术和农业食品开发替代职业道路，为传统上专注于生物医学应用的英国生物信息学社区开辟新的机会。

项目成果

Plant specimen contextual data consensus.

植物标本上下文数据共识。

• DOI: 10.1093/gigascience/giw002
• 发表时间: 2016-12-01
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Hoopen PT;Walls RL;Cannon EK;Cochrane G;Cole J;Johnston A;Karsch-Mizrachi I;Yilmaz P
• 通讯作者: Yilmaz P

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

• DOI: 10.1093/nar/gkv1045
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Petryszak R;Keays M;Tang YA;Fonseca NA;Barrera E;Burdett T;Füllgrabe A;Fuentes AM;Jupp S;Koskinen S;Mannion O;Huerta L;Megy K;Snow C;Williams E;Barzine M;Hastings E;Weisser H;Wright J;Jaiswal P;Huber W;Choudhary J;Parkinson HE;Brazma A
• 通讯作者: Brazma A

Ensembl 2017.

• DOI: 10.1093/nar/gkw1104
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Aken BL;Achuthan P;Akanni W;Amode MR;Bernsdorff F;Bhai J;Billis K;Carvalho-Silva D;Cummins C;Clapham P;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Juettemann T;Keenan S;Laird MR;Lavidas I;Maurel T;McLaren W;Moore B;Murphy DN;Nag R;Newman V;Nuhn M;Ong CK;Parker A;Patricio M;Riat HS;Sheppard D;Sparrow H;Taylor K;Thormann A;Vullo A;Walts B;Wilder SP;Zadissa A;Kostadima M;Martin FJ;Muffato M;Perry E;Ruffier M;Staines DM;Trevanion SJ;Cunningham F;Yates A;Zerbino DR;Flicek P
• 通讯作者: Flicek P

Ensembl Genomes 2016: more genomes, more complexity.

• DOI: 10.1093/nar/gkv1209
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kersey PJ;Allen JE;Armean I;Boddu S;Bolt BJ;Carvalho-Silva D;Christensen M;Davis P;Falin LJ;Grabmueller C;Humphrey J;Kerhornou A;Khobova J;Aranganathan NK;Langridge N;Lowy E;McDowall MD;Maheswari U;Nuhn M;Ong CK;Overduin B;Paulini M;Pedro H;Perry E;Spudich G;Tapanari E;Walts B;Williams G;Tello-Ruiz M;Stein J;Wei S;Ware D;Bolser DM;Howe KL;Kulesha E;Lawson D;Maslen G;Staines DM
• 通讯作者: Staines DM

Ensembl 2016.

• DOI: 10.1093/nar/gkv1157
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Yates A;Akanni W;Amode MR;Barrell D;Billis K;Carvalho-Silva D;Cummins C;Clapham P;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Johnson N;Juettemann T;Keenan S;Lavidas I;Martin FJ;Maurel T;McLaren W;Murphy DN;Nag R;Nuhn M;Parker A;Patricio M;Pignatelli M;Rahtz M;Riat HS;Sheppard D;Taylor K;Thormann A;Vullo A;Wilder SP;Zadissa A;Birney E;Harrow J;Muffato M;Perry E;Ruffier M;Spudich G;Trevanion SJ;Cunningham F;Aken BL;Zerbino DR;Flicek P
• 通讯作者: Flicek P