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.

中国境内已确认存在数十个登记在册的本土犬种，但目前针对这些犬种的种群结构、基因组连锁不平衡（linkage disequilibrium, LD）模式以及选择印记的系统性研究仍较为匮乏。本研究系统性地对来自15个不同中国本土犬种的169只无亲缘关系犬只的基因组进行了检测分析。研究采用犬类170K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片，对中国与西方犬类的基因组结构开展对比分析；其中西方犬类的170K SNP芯片基因分型数据下载自LUPA（欧洲犬类基因组计划倡议）数据库。中国本土犬类的基因组连锁不平衡程度更低，纯合子片段（runs of homozygosity, ROH）的累计长度更短。各中国本土犬种内个体间的遗传距离显著大于西方犬种内部的个体遗传距离。主成分分析（Principal Component Analysis, PCA）与邻接（neighbor-joining, NJ）系统发育树分析结果表明，中国与西方犬类存在明显的系统发育亲缘分化。本研究发现西方犬类曾向中国哈萨克牧羊犬与蒙古细犬发生历史基因渐渗的证据。同时本研究提出，格陵兰雪橇犬、西班牙蝴蝶犬以及欧洲欧亚犬中携带有中国犬类的血统谱系。全基因组统计分析鉴定出了各中国本土犬种以及三个犬种组的全基因组选择印记。本研究筛选出多个经历自然选择的候选基因，这些基因或与犬种典型表型特征的形成密切相关。其中，EPAS1与DNAH9等基因在青藏高原犬类中呈现自然选择特征，这类基因对于高海拔环境的遗传适应具有重要作用。RBP7、NMNAT1、SLC2A5以及H6PD基因在中国山地猎犬中呈现自然选择印记，这类基因或与狩猎能力（耐力与夜视能力）相关。此外，选择性清除分析显示，NOL8、KRT9、RORB与CAMTA1或为影响犬只奔跑速度的候选基因。本研究关于中国本土犬类基因组与种群结构、以及选择印记的研究结果，进一步佐证了中国本土犬类拥有丰富的表型多样性，是鉴定复杂性状相关基因的重要遗传资源。