Affymetrix SNP array data for beak deformity and normal Beijing-You Chickens

Beak deformities (BD) of different forms have been documented in many wild birds. The phenomenon is termed as “the largest epizootic of gross abnormalities ever recorded among wild bird populations.” Frequencies of 1% to 3% of BD (crossed beaks) were found in several indigenous chickens including Silkies, Qingyuan Partridge, Huxu, and the Beijing-You (BJY) chickens (studied here). Birds with deformed beaks have poor production performance and induce higher mortality. Therefore, BD represents an economic as well as a welfare problem. Our lab have focused and performed studies on this complex trait/disease for 7 years. Therefore, we performed a single SNP, a pathways-based genome-wide association study (GWAS), and a genome-wide CNV detection with the genotype data of 48 BD (case) and 48 normal (control) birds from Affymetrix 600K HD genotyping arrays, using ROADTRIPS, SNP ratio test (SRT) and PennCNV, respectively. To the best of our knowledge, this is the first GWAS and CNV study to investigate the mutations and genomic structural variations in the deformed and normal beaks of chickens. The findings herein are worth of further functional characterization for better understanding the genetic mechanisms of BD in chickens and wild birds as well. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples. GWAS and Copy number analysis of Affymetrix 600K chicken SNP arrays were performed for all the samples.