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

<p><span><span><span><span><span><span><span><span><span><span><span><a name="_Hlk15722205">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. </a>Here, <a name="_Hlk15722444">we systematically surveyed the genomes </a>of 169 unrelated dogs that were from<a name="_Hlk15722467">15 diverse Chinese dog breeds</a>. Canine 170K SNP chips were used to<a name="_Hlk15722535">compare the genomic structures of Chinese and Western dogs</a>. 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. <a name="_Hlk15722638">We found evidence for historical introgression of Western dogs</a>into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Spanish Papillon, and European Eurasier have Chinese dog lineages. The <i>d_i</i>statistic 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. <i>EPAS1</i>and <i>DNAH9</i>, showed signatures of natural selection in Qinghai-Tibetan plateau dogs and are important for genetic adaptation to high altitude. <i>RBP7</i>,<i>NMNAT1</i>,<i>SLC2A5,</i>and <i>H6PD</i>genes 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 <i>NOL8</i>,<i>KRT9</i>, <i>RORB</i>and <i>CAMTA1</i>might be candidate genes for dog running speed. The resultsabout genomic and population structures, and <a name="_Hlk15722685">selection signatures of Chinese dog breeds reinforce the conclusion that </a>Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.</span></span></span></span></span></span></span></span></span></span></span></p>