A Case Control GWAS for APEC in a Commercial Broiler Cross

We performed genome wide association tests for susceptibility to Avian Pathogenic Escherichia Coli (APEC) in 1119 case and 982 control birds from a commercial broiler cross, collected at a Danish abattoir. Cases were identified by visual inspection by trained veterinarians as animals showing APEC cellulitis and bacteriologically verified. Birds were genotyped with an Illumina’s 41k chicken chip with optimized cluster solutions for our sample. After filtering for MAF > 0.02 and call rate > 0.95, 26,614 SNPs remained on gga1-gga28 for analysis. Haplotypes coming from each of the parental lines in windows of 20 markers were identified using a custom written hidden Markov model. 26,105, 24,346 and 24,014 SNPs with MAF > 2% within lines remained for association testing in each of the parental lines, respectively. Association testing of deconvoluted haplotypes within each of the parental lines and for convoluted genotypes across lines was performed with SVS7.6.4. Several regions met genome wide significance after multiple testing corrections using haplotype based per block and per haplotype analysis of 3-SNP-haplotypes. Across line mapping with convoluted genotypes did not yield genome significant regions after multiple testing corrections, but the regions identified in single line analyses could be confirmed as regions of elevated test statistic signals. The most promising regions on GGA1, 3, 5, 6 and 11 are being further investigated to refine and validate identified signals. To our knowledge this is the first attempt to map QTLs segregating in the parental lines using crossbred commercial offspring. Acknowledgement. Funded by EC-FP7/2007-2013, agreement n°222664, “Quantomics”.