High-Density Genotyping of Chicken Populations

Genomic DNA was extracted from 1.5-mL blood samples using DNeasy 96 Blood & Tissue Kits (QIAGEN, Germany). A total of 1078 hens were genotyped with the Chicken 600 K SNP array [42 (link)] (Affymetrix, Inc. Santa Clara, CA, USA) which contained 580,961 SNPs across 28 autosomes and two sex chromosomes. We first discarded 6593 SNPs with unknown physical position and repeated genomic coordinates. The Affymetrix Power Tools v1.19.0 (APT) software was then implemented to control the quality of sample call rate (> 97%) and dish quality (> 0.82). After the quality control, 1063 individuals and 517,856 SNPs remained. In addition, the low quality of SNPs (SNP call rate < 95%, minor allele frequency < 0.01, Hardy-Weinberg equilibrium P < 1 × 10–6) were filtered out through the PLINK package [43 (link)]. The remaining SNPs with missing genotypes were imputed using the Beagle v4.0 procedure [44 (link)]. Finally, a total of 1063 individuals and 294,705 SNPs located on autosomes (Additional file 4: Table S2) were deemed eligible for the following analyses.