Identification of single nucleotide polymorphisms underlying the strength of lysozyme activity in chicken, a genome-wide association study

Using the Illumina 60k SNP chip panel, a genome-wide association study was carried out in order to identify genomic regions underlying lysozyme activity in chicken. Data were collected from an F2 chicken population originated from reciprocal crosses between Arian broiler line and West Azerbaijan indigenous chicken strains. In this study, the lysozyme activity against Micrococus luteus bacteria, recorded as an indicator for innate immunity. Statistical analysis was based on fixed and mixed linear models to account for population stratifications and avoiding systematic biases generated from sex and hatch. Correction for multiple testing was done by applying a 10% genome-wise false discovery rates as significant threshold. Results showed that in both statistical models three markers of GGaluGA206187, rs16479594 and rs15204127, located on chromosomes 3, 5 and 1 respectively have significant associations with innate immunity in chicken (FDR<0/1). The finding are in agreement with previous published studies. Subsequent gene enrichment analysis in DAVID database underpin that candidate genes flanking these three regions of the genome have considerable roles in nine biochemical pathways with pivotal effects on the function of immune system.