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

草地是英国的主要作物，而多年生黑麦草（Lolium perenne）是大部分草地的单一、最重要的组成部分。总的来说，英国的草地占土地面积的50%以上，占所有农业用地的70%，2006年英国农业草地的市场价值，以肉类和牛奶产量来衡量，估计为48亿英镑。除了传统的农业用途外，草和草地在包括运动场和景观美化在内的宜人环境中也具有重要意义，而且人们对开发替代草地用途的兴趣也越来越大，例如用于生物燃料和平台化学品生产。IBERS是英国黑麦草育种/种质资源的主要中心，也是生物能源草改良的重点。它有一个成熟的基础设施，允许植物遗传学、基因组学、生理学、生物化学和环境分析研究与育种和可持续性目标相互作用，因此，它在开发新的基因组技术方面处于独特的地位。草类科学家的一个主要目标是能够确定在决定这些作物的目标性状中起重要作用的基因组区域，因为我们影响这些性状的能力(例如。（如耐旱性/耐热性、氮利用效率、开花、生物能性状）是维持可持续草地的基础。全面基因组分析的一个重要步骤是建立物理图谱。这涉及到一些连续的过程：a)开发广泛的大插入（BAC）基因组DNA文库，有效地将基因组片段和分割成可以编目的小片段。B)生成每个bac的独特“指纹”。C)通过识别重叠的指纹模式（连续克隆或contigs）来确定基因组中bac的物理顺序。D)将已识别的组合与现有的基因或染色体图联系起来。通过对每个bac的末端进行测序，可以获得额外的信息。该信息可用于确认重叠指纹模式和帮助确定基因组结构。结果是基因组被分解成一系列有序的可管理的片段。这些可用于基因组特定区域的靶向DNA测序或大规模全基因组测序。本研究的目的是为草和其他单子叶植物研究人员开发这一资源，以便更好地了解基因组结构和功能。为了使这些信息广泛可用，将开发一个开放访问的网络界面，它将显示项目的进展，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。

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.