High resolution, advanced intercross mapping of host resistance to Salmonella colonization

Availability of a dense single-nucleotide polymorphism (SNP) map in chickens has allowed for whole-genome QTL mapping for disease resistance. In this study, two F8 advanced intercross lines of broiler by Fayoumi and broiler by Leghorn chickens, and a dense, genome-wide SNP panel were used to map genomic regions associated with host resistance to bacterial colonisation. One week after inoculation of day-old chicks with Salmonella enteritidis (SE), caecum and spleen tissues were collected to quantitate the bacterial load. Of 2733 genotyped SNPs, 875 were homozygous and the remaining SNPs with a minor allele frequency of > 0.2 were individually tested for association with SE burden by utilising a Chi-square log-likelihood test between models with and without SNP genotype. Using a Q-value of 25%, calculated utilising 1207 SNPs with Chi-square P-Value < 1.0 to control for false discovery, 21 SNPs identifying 19 genes were significantly associated with SE bacterial levels. Ten genes were in pathways associated with immune response to Salmonella (toll-like receptor signaling, apoptosis, and MAPK signaling), further supporting their involvement in host resistance pathways. In addition to identifying new candidate genes for bacterial resistance, the trait-associated SNPs may be useful in marker assisted selection programmes for disease resistance.