Genome-Wide Association Study for meat quality traits in an F2 intercross between Azerbaijan native chickens and Ariyan broiler line

In order to identify loci and genes associated with meat quality traits, genome-wide association study (GWAS) were conducted in a F2 population derived from a reciprocal cross between Azerbaijan native chickens and Aryan broiler line by using Illumnia 60 K Chicken SNP Bead chip. For each bird, a total 6 traits including water holding capacity, meat color lightness (L*), redness (a*), yellowness (b*), shear force and ultimate pH were measured. The SNPs that were associated with meat quality traits were identified using both GLM and compressed mixed linear models (CMLM). A total of 36 SNPs were associated with meat quality traits in the genome–wide significance and suggestive levels, that 3 SNPs were significantly associated with meat color yellowness through CMLM model and 18 SNPs were suggestively associated with meat color yellowness, ultimate pH, water holding capacity and shear force through GLM model. The identified candidate genes have molecular functions related to meat quality traits. So, these candidate genes can be applied in the chicken breeding scheme.