DOI: 10.5061/dryad.76hdr7srv
title: Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs

description: 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 distatistic 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.
description: 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 <i>vs.</i>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).