There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 169 unrelated dogs that were from15 diverse Chinese dog breeds. Canine 170K SNP chips were used tocompare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogswere downloadedfrom the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Principal component analysis (PCA) and neighbor-joining (NJ)-tree analysis indicated distinct phylogenetic affinities between Chinese and Western dogs. We found evidence for historical introgression of Western dogsinto Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Spanish Papillon, and European Eurasier have Chinese dog lineages. The d_istatistic estimation identified genome-wide selection signatures of each Chinese breed and three breed groups. This study highlights several candidate genes that have undergone natural selection and might be responsible for breed-typical phenotypes. Several genes, e.g. EPAS1and DNAH9, showed signatures of natural selection in Qinghai-Tibetan plateau dogs and are important for genetic adaptation to high altitude. RBP7,NMNAT1,SLC2A5,and H6PDgenes exhibit signatures of natural selection in Chinese mountain hounds and are likely associated with hunting abilities (endurance and night vision). Moreover, the selective sweep analysis suggested that NOL8,KRT9, RORBand CAMTA1might be candidate genes for dog running speed. The resultsabout genomic and population structures, and selection signatures of Chinese dog breeds reinforce the conclusion that Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.

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).