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Background   Campylobacter  is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to  Campylobacter  could potentially reduce its subsequent entry into the food chain.  Campylobacter  intestinal colonisation levels are influenced by the host genetics of the chicken. In the present study, two chicken populations were used to investigate the genetic architecture of avian resistance to colonisation: (i) a back-cross of two White Leghorn derived inbred lines [(6 1  x N) x N] known to differ in resistance to  Campylobacter  colonisation and (ii) a 9 th  generation advanced intercross (6 1  x N) line.    Results  The level of colonisation with  Campylobacter jejuni  following experimental infection was found to be a quantitative trait. A back-cross experiment using 1,243 fully informative single nucleotide polymorphism (SNP) markers revealed quantitative trait loci (QTL) on chromosomes 7, 11 and 14. In the advanced intercross line study, the location of the QTL on chromosome 14 was confirmed and refined and two new QTLs were identified located on chromosomes 4 and 16. Pathway and re-sequencing data analysis of the genes located in the QTL candidate regions identified potential pathways, networks and candidate resistance genes. Finally, gene expression analyses were performed for some of the candidate resistance genes to support the results.    Conclusion   Campylobacter  resistance in chickens is a complex trait, possibly involving the Major Histocompatibility Complex, innate and adaptive immune responses, cadherins and other factors. Two of the QTLs for  Campylobacter  resistance are co-located with  Salmonella  resistance loci, indicating that it may be possible to breed simultaneously for enhanced resistance to both zoonoses.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2612-7) contains supplementary material, which is available to authorized users.

The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens