In Chapter 2, a directed linkage scam for loci involved in body weight and carcass composition traits is performed in a commercial Charollais sheep population. Five chromosomes were investigated based on prior evidence for major genes effecting the studied traits in other breeds. A maximum likelihood variance component analysis using identity-by-descent values estimated by Markov chain Monte Carlo methods was performed on a complex pedigree containing a total of 570 sheep. Of the total of nine QTL detected, the estimated position of only one overlapped with the regions showing major genes that were used in chromosome selection. During the analysis of the Charollais sheep population, a region of the genome showing a significant deviation from the published sheep linkage map was detected. This region is examined in more detail in Chapter 3, with the addition of further microsatellite markers as well as the investigation of this region in two further sheep breeds. With the inclusion of the published linkage map, this demonstrated a total of three linkage maps across four populations. Such heterogeneity in linkage maps across sheep breeds has important consequences for the design and analysis fine-mapping studies. The significance of a QTL linkage peak is not readily evaluated with general pedigrees. The extension of permutation methodology that is commonly used with structured pedigrees to more general pedigrees is investigated in Chapter 4. Chapter 5 examines the population dynamics of a well studied wild Soay sheep population. A unified statistical framework is developed for all major aspects of the life cycle of the sheep. This forms the basis of a simulation model of the population that is used to predict the amount of linkage disequilibrium in the population (Chapter 6) and the effective population size of the population (Chapter 7). The examination of the linkage disequilibrium structure in a population is an important step in the design of studies with the aim of fine-mapping quantitative trait loci. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping. Through the use of the simulation model, the effective population size of the Soay sheep population was estimated to be approximately 0.17 of its census population size. This is approximately half the value obtained with the use of a general predictive equation.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:657645 |
| Date | January 2005 |
| Creators | McRae, Allan F. |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/15362 |
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