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

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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.