McCarthy, Linda Catherine; (1995) New approaches to genome mapping in model organisms. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

This object of this thesis was to develop new genome mapping strategies and techniques, and apply these to both the fission yeast Schizosaccharomyces pombe genome and the mouse genome. I describe complete physical mapping of the S. pombe genome, and the global genetic mapping of the mouse genome using a hybridisation based approach. The S. pombe genome was used as a test system to develop large-scale global genome mapping techniques which could be effectively applied to mammalian genome projects. The lessons learned from the S. pombe mapping project were then applied to the mouse genome project, leading to an integrated genetic and physical mapping strategy for global mouse genome mapping. These lessons included the optimal efficiency obtained from using hybridisation assays to generate the mapping data, as well as the importance of a dense high resolution genetic map of hybridisation probes for efficient and inexpensive global physical mapping. Interspersed repetitive elements were exploited to develop a novel high resolution genetic mapping technique in the mouse. Interspersed Repetitive Element PCR (IRS-PCR) uses primers to interspersed repetitive elements to generate pools of tens of thousands of different PCR products, containing non-repetitive sequence occurring between repetitive elements. The IRS-PCR product mapping approach has the advantages of being inexpensive and fast, as well as taking no more effort to map the probes on 1,000 animals than it would to map them on 20. This allows all the IRS-PCR product probes to be mapped to the same high resolution, with no greater effort or expense than would be required to establish the weakest linkage. This integrated genetic and physical mapping approach quickly generates genetically anchored YAC contigs, located randomly across the genome. Gap closure between these contigs could then be achieved by hybridising YAC PCR products back to the YAC library filters. A high resolution genetic map with a marker every 500 kb, should quickly identify mixed- chromosome contigs generated by chimeric YACs. A first generation mouse genetic map containing over 180 IRS-PCR product markers is presented, along with hybridisation data to the YAC library and polymorphism rates of these probes across 39 rodent strains.

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