Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs

We genotyped 172 dogs, including 156 dogs from 15 Chinese indigenous dog breeds, 10 Rottweiler as controls, 3 Papillonsand 3 Asian wolves. In addition, the 170K SNP genotyping data of 456 Western dogs was from the dataset generated by the LUPA consortium. All 172 samples were genotyped using Canine 170K SNP BeadChips(containing 173,662 SNPs) on an iScan System (Illumina, USA). The examined SNPs in the dataset downloaded was slightly different from our data because the versions of BeadChips were different, and SNP positions were annotated using different reference genome assemblies (v3.0 vs.v2.0). To deal with these differences, the 120-bp flanking sequences for all SNPs in the downloaded dataset were extracted. And then, these short sequences were mapped to the dog reference genome assembly (v3.0) to identify the common SNPs between the two versions of chips and determined their positional information (Kent, 2002). A common subset data (151,057 SNP markers) was obtained for further analysis using PLINK (v1.9).