Abstract
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 157 unrelated dogs that were from 15 diverse Chinese dog breeds. Canine 170K SNP chips were used to compare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogs were downloaded from 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. Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree. We found evidence for historical introgression of Western dogs into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Papillon, and European Eurasier have Chinese dog lineages. Selection sweep analysis identified genome-wide selection signatures of each Chinese breed and three breed groups. We highlighted several genes including EPAS1 and DNAH9 that show signatures of natural selection in Qinghai-Tibetan plateau dogs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports suggested RBP7, NMNAT1, SLC2A5, and H6PD that exhibit signatures of natural selection in Chinese mountain hounds as promising candidate genes for the traits of endurance and night vision, and NOL8, KRT9, RORB, and CAMTA1 that show signals of selection in Xi dogs might be candidate genes influencing dog running speed. The results about 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.
Highlights
Of all the domesticated animals, dogs (Canis familiaris), are one of the most popular species
We investigated the population structure, genetic diversity, and linkage disequilibrium (LD) extent of 15 Chinese indigenous dog breeds using the 170K SNP chips
From the results of genetic diversity analysis, we suggest that Chinese indigenous dogs have higher levels of genetic diversity compared with Western dogs
Summary
Of all the domesticated animals, dogs (Canis familiaris), are one of the most popular species. The first stage occurred over 15,000 years ago The dogs in this stage came from a population of wolf-like progenitors. There are many speculations about what wolf species was the origin of domestic dog. Scientists from Switzerland and China claim that dogs originated from the Asian Grey Wolf in Southeast Asia over 33,000 years ago (Leonard et al, 2002; Savolainen et al, 2002). Shannon et al (Shannon et al, 2015) published an alternative origin story and suggested that domestic dogs originated from central Asia. This conclusion was based on autosomal, mitochondrial, and Y chromosome diversity data from 4,676 purebred dogs (161 breeds, 549 cities, and 38 countries). The geographic and temporal origins of domestic dogs remain controversial
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