Gene hunting: molecular analysis of the chicken genome

This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput screening of resource populations. The markers can be divided in markers located within chicken genes or ESTs (type I markers) and random markers (type II). The microsatellite markers (430) were subsequently used for the development of a highly informative comprehensive linkage map of the chicken genome. The type I markers provide the necessary links to create a comparative map between chicken and human. A further step in the analysis of the chicken genome is the construction of a physical map and the improvement of the chicken-human comparative map.Therefore a chicken Bacterial Artificial Chromosome (BAC) library was constructed with a 5.5x genome coverage and an average insert size of the BAC clones of 134 kb. Physical mapping was performed by building a BAC contig of chromosome 10 by chromosome walking. Using a bi-directional approach that utilizes the information from the chicken as well as the human genome, a detailed comparative map was obtained for chicken chromosome10 and human chromosome 15. This approach involved sample sequencing of BAC clones as well as FISH mapping. The STS markers developed for chromosome walking are currently used for the development of SNP markers, which will subsequently be used in the advanced intercross lines of the Wageningen resource population to narrow down the chromosomal regions containing the QTL. This information together with a very detailed comparative map will allow the identification of candidate genes for these particular QTL.