Validation of Whole Genome Resequencing for Mapping the Genetics of Ascites in Broilers and Viral Susceptibility in Layers

This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers with no negative impact on bird growth while some growth characteristics even improved in the MAS genetic line. With the success of the MAS project and improvements in the bioinformatic pipeline, a new WGR project was conducted and is discussed in Chapter 3. The goal of the project was to assess whether WGR could map genetic determinants of resistance to infectious bronchitis virus in white leghorn chickens. The results of this project revealed a genetic region with strong potential for MAS in white leghorn chickens which could increase innate resistance in those birds. As a whole, this work supports the effectiveness of WGR as a powerful tool in the detection of genetic variability associated with disease resistance