Developing a physical map of the Lolium perenne genome based on high-information content BAC fingerprinting and BAC-end sequencing

基于高信息含量 BAC 指纹识别和 BAC 末端测序开发黑麦草基因组物理图谱

基本信息

批准号：
BB/G012342/1
负责人：
Ian Armstead
金额：
$ 184.2万
依托单位：
Aberystwyth University
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2010
资助国家：
英国
起止时间：
2010 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FG012342%2F1
关键词：
Developing physical map Lolium perenne

项目摘要

Grassland is a predominant crop in the UK and Lolium perenne (perennial ryegrass) is the single, most significant component of the majority of this grassland. In total, UK grasslands account for more than 50% of the land area and 70% of all agricultural land use and the market value of UK agricultural grassland in 2006, measured in terms of meat and milk production, is estimated to have been c. £4.8 billion. In addition to conventional agricultural use, grass and grasslands are of fundamental importance in amenity situations, including sports fields and landscaping, and there is also increasing interest in the development of alternative grassland uses, such as for biofuel and platform chemical production. IBERS is the major centre for ryegrass breeding/germplasm resources within the UK as well as being the focus of bioenergy grass improvement. It has an established infrastructure allowing the interplay of research in plant genetics, genomics, physiology, biochemistry and environmental analysis with breeding and sustainability objectives, thus, it is in a unique position to exploit new genome technologies. A major aim of grass scientists is to be able to define genomic regions that play an important role in determining target traits in these crops, as our ability to influence these traits (eg., drought/heat tolerance, nitrogen use efficiency, flowering, bioenergy traits) is fundamental to maintaining sustainable grasslands. A major step in comprehensive genome analysis is the establishment of a physical map. This involves a number of sequential processes: A) Develop extensive large-insert (BAC) genomic DNA libraries which, effectively, fragment and partition the genome into smaller pieces which can be catalogued. B) Generate distinctive 'fingerprints' of each of these BACs. C) Define the physical order of BACs within the genome by identifying overlapping fingerprint patterns (contiguous clones, or contigs). D) Relate the identified contigs to existing genetic or chromosome maps. Extra information can be obtained by sequencing the ends of each of the BACs. This information can be used in confirming overlapping fingerprint patterns and in helping to define the genome structure. The outcome is that the genome is broken down into an ordered series of manageable fragments. These can be used for targeted DNA sequencing of particular regions of the genome / or for large scale whole genome sequencing. The aim of this research is to develop this resource for grass and other monocot researchers to enable a greater understanding of the genome structure and function. In order to make this information widely available, an open-access web-interface will be developed which will display progress in the project and allow for the raw data to be downloaded, so that other researchers can use it in their own analyses.

草原是英国的主要作物，而洛里姆·佩伦（Lolium Perenne）（多年生黑麦草）是大多数草原的单一组成部分。总共，英国草原占土地面积的50％以上，占所有农业土地利用的70％，2006年英国农业草地的市场价值估计是肉类和牛奶的生产来衡量的。 48亿英镑。除了传统的农业用途外，在包括运动场和园林绿化在内的舒适情况下，草和草原至关重要，并且对替代草地用途（例如生物燃料和平台化学生产）的发展也越来越兴趣。 ibers是英国黑麦草繁殖/种质资源的主要中心，也是生物能量草的重点。它具有既定的基础设施，允许在植物遗传学，基因组学，生理学，生物化学和环境分析中与育种和可持续性目标进行研究的相互作用，因此，利用新的基因组技术是一个独特的立场。草科学家的一个主要目的是能够定义基因组区域，这些区域在确定这些作物中的目标特征方面起着重要作用，因为我们影响这些特征的能力（例如，干旱/耐热耐受性，氮气使用效率，开花，生物能特征）是维持可持续草原的基本性。综合基因组分析的主要步骤是建立物理图。这涉及许多顺序过程：a）开发广泛的大插入（BAC）基因组DNA文库，从而有效地将基因组分解为可以分类的较小片段。 b）产生这些BAC中每个BAC的独特“指纹”。 c）通过识别重叠的指纹模式（连续D）将BAC在基因组中的物理顺序与现有的遗传或染色体图相关联。可以通过对每个BAC的末端进行测序获得额外的信息。这些信息可用于确认重叠的指纹模式并帮助定义基因组结构。结果是，基因组分为有序的一系列可管理的片段。这些可用于基因组的特定区域的靶向DNA测序，或用于大规模的整个基因组测序。这项研究的目的是为草和其他单子弹研究人员开发此资源，以使对基因组结构和功能有更深入的了解。为了使此信息广泛可用，将开发一个开放访问网络接口，将在项目中显示进度并允许下载原始数据，以便其他研究人员可以在自己的分析中使用它。

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）

Emerging knowledge from genome sequencing of model plants and fodder crops

来自模式植物和饲料作物基因组测序的新兴知识

DOI：
发表时间：
2014
期刊：
影响因子：
0
作者：
6. Mikic M
通讯作者：
6. Mikic M

Genomic regulation of plant mating systems: flexibility and adaptative potential. A commentary on: 'A new genetic locus for self-compatibility in the outcrossing grass species perennial ryegrass ( Lolium perenne )'

植物交配系统的基因组调控：灵活性和适应潜力。

DOI：
10.1093/aob/mcab024
发表时间：
2021
期刊：
Annals of Botany
影响因子：
4.2
作者：
Mable B
通讯作者：
Mable B

Characterization and practical use of self-compatibility in outcrossing grass species.

DOI：
10.1093/aob/mcab043
发表时间：
2021-06-24
期刊：
Annals of botany
影响因子：
4.2
作者：
Cropano C;Place I;Manzanares C;Do Canto J;Lübberstedt T;Studer B;Thorogood D
通讯作者：
Thorogood D

Developing a physical map of the Lolium perenne genome based on High-Information Content BAC Fingerprinting and BAC-end sequencing.

基于高信息含量 BAC 指纹图谱和 BAC 末端测序开发黑麦草基因组物理图谱。