Chicken genome mapping - Constructing part of a road map for mining this bird's DNA
The aim of the research presented in this thesis was to aid in the international chicken genome mapping effort. To this purpose, a significant contribution was made to the construction of the chicken whole-genome BAC-based physical map (presented in Chapter A). An important aspect of this construction was the integration of the genetic and physical maps (see Chapters 2 and 3) in order to anchor clone-contigs to a chromosomal location.In addition to the construction of the physical map, two different SNP resources were analyzed. First, it is shown in Chapter 5 that cione-based sequencing is a valid SNP discovery strategy. Second, an anaLysis of public SNP repositories was presented, focussing on intra-genic SNP discovery in human (Chapter 6) which pinpointed some issues related to mining public SNP databases. In Chapter 7, the extent of linkage disequiiibrium -~ reflecting the history of recombinations - was assessed in two regions of the chicken genome. This information is useful for setting up linkage and association studies. Finally, a software tool was described (Chapter 8) that was implemented to automate the analysis of sequencing data, which is especially important in major mapping experiments as described in this thesis.
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| Format: | Doctoral thesis biblioteca |
| Language: | English |
| Subjects: | dna sequencing, fowls, gene mapping, genetic mapping, genetics, genome analysis, linkage, dna-sequencing, genetica, genetische kartering, genkartering, genoomanalyse, kippen, koppeling, |
| Online Access: | https://research.wur.nl/en/publications/chicken-genome-mapping-constructing-part-of-a-road-map-for-mining |
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| Summary: | The aim of the research presented in this thesis was to aid in the international chicken genome mapping effort. To this purpose, a significant contribution was made to the construction of the chicken whole-genome BAC-based physical map (presented in Chapter A). An important aspect of this construction was the integration of the genetic and physical maps (see Chapters 2 and 3) in order to anchor clone-contigs to a chromosomal location.In addition to the construction of the physical map, two different SNP resources were analyzed. First, it is shown in Chapter 5 that cione-based sequencing is a valid SNP discovery strategy. Second, an anaLysis of public SNP repositories was presented, focussing on intra-genic SNP discovery in human (Chapter 6) which pinpointed some issues related to mining public SNP databases. In Chapter 7, the extent of linkage disequiiibrium -~ reflecting the history of recombinations - was assessed in two regions of the chicken genome. This information is useful for setting up linkage and association studies. Finally, a software tool was described (Chapter 8) that was implemented to automate the analysis of sequencing data, which is especially important in major mapping experiments as described in this thesis. |
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