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

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.