Detection of genomic regions containing genes that affect economic traits is a primary step for potential improvements of livestock through marker-assisted selection. Salmonella enteritidis (SE) bacterial burden and SE vaccine antibody production are examples of important traits in commercial chickens. A main objective of the research presented herein was to identify single nucleotide polymorphisms (SNPs) associated with SE bacterial burden in either the spleen or cecum and vaccine antibody levels of young chickens through the use of multiple levels of genotyping platforms. Another objective was to compare linkage disequilibrium levels present prior to and after implementation of an advanced intercrossing mating scheme. SNPs within the Gallinacin gene cluster were genotyped on an F1 cross between four broiler sires and two inbred dam lines (Fayoumi and Leghorn), and were analyzed for association with SE bacterial burden in the spleen and cecal content and vaccine antibody response. The use of individual candidate gene studies identified two potential markers (SNPs in Gal3 and Gal7) for marker-assisted selection for SE vaccine antibody response. A subsequent study was performed on the Gallinacin genes through the use of the SNaPshot genotyping platform and utilizing two separate F8 advanced intercross lines (AIL) to examine SE bacterial burden response. Five SNPs showed association at P\u3c0.05, with three clustering between Gal11-13 (3-SNP haplotype P\u3c0.008). The haplotype indicates the Gal11-13 region is a strong candidate for SE response. Using a high-density SNP array to genotype 2733 SNPs, a linkage disequilibrium (LD) fine mapping study was conducted to examine the change in LD between an F2 and two F8 AIL populations. LD levels were reduced 1.5-fold from the F2 to F8 AIL populations. The reduction illustrates the potential gain of utilizing the advanced intercross mating scheme for future association studies. Using 3000 SNPS, associations with SE bacterial burden were examined. Twenty-one markers in nineteen genes were identified at P\u3c0.02 with SE burden. These genes confirmed previously identified biological pathways important in response to bacterial infections in livestock. The molecular markers and reduction in LD identified provides an integral step in improvement of SE resistance in commercial birds through marker-assisted selection programs
