Table_4_Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs.xlsx

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.

中国拥有数十个经认可的本土犬品种，但目前针对这些品种的种群结构、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个不同中国本土犬品种的157只无亲缘关系犬只的基因组进行了检测分析。我们使用犬类170K SNP芯片对中国与西方犬类的基因组结构开展比较研究，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项目）数据库。分析结果显示，中国本土犬类的基因组连锁不平衡程度更低，连续纯合片段（runs of homozygosity, ROH）的累积长度也更短；中国各犬品种内部个体间的遗传距离大于西方犬品种。通过主成分分析（PCA）与邻接树（NJ-tree）分析可见，中国本土犬与西方犬品种清晰地划分为两个独立演化支。本研究发现了西方犬类曾向中国哈萨克牧羊犬与蒙古Xi犬发生历史基因渐渗的证据；同时推测格陵兰雪橇犬（Greenland sledge dog）、蝶耳犬（Papillon）以及欧洲欧亚犬（European Eurasier）携带有中国犬的血统。选择清除分析鉴定出了各中国犬品种以及三个品种群的全基因组选择印记。我们重点关注了EPAS1与DNAH9等多个基因，这些基因在青藏高原犬中呈现自然选择印记，可能与高海拔环境的遗传适应密切相关。将本研究结果与既往报道进行比对后发现：在中国山地猎犬中呈现自然选择印记的RBP7、NMNAT1、SLC2A5与H6PD基因，可作为耐力与夜视性状的潜在候选基因；而在Xi犬中检测到选择信号的NOL8、KRT9、RORB与CAMTA1基因，则可能是影响犬只奔跑速度的候选基因。针对中国犬品种的基因组与种群结构以及选择印记的研究结果进一步证实：表型多样性丰富的中国本土犬，是鉴定复杂性状相关基因的重要遗传资源。