Liu Shuqin, Yang Yunzhou, Pan Qingjie, Sun Yujiang, Ma Hongying, Liu Yu, Wang Min, Zhao Chunjiang, Wu Changxin
College of Animal Science and Technology, China Agricultural University, Beijing, China.
Equine Center, China Agricultural University, Beijing, China.
Front Genet. 2020 May 21;11:467. doi: 10.3389/fgene.2020.00467. eCollection 2020.
Extremely low nucleotide diversity of modern horse Y-chromosome has been reported, and only poor phylogenetic resolution could be resulted from limited Y-chromosome markers. In this study, three types of horse Y-chromosome markers, including Single-nucleotide polymorphisms (SNPs), copy number variants (CNVs), and allele-specific CNVs, were developed by screening more than 300 male horses from 23 indigenous Chinese horse populations and 4 imported horse breeds. Fourteen segregating sites including a novel SNP in the AMELY gene were found in approximately 53 kb of male-specific Y-chromosome sequences. CNVs were detected at 11 of 14 sites, while allele-specific CNVs at 6 polymorphic sites in repeated fragments were also determined. The phylogenetic analyses with the SNPs identified in this study and previously published 51 SNPs obtained mainly from European horses showed that indigenous Chinese horses exhibit much deeper divergence than European and Middle Eastern horses, while individuals of Chinese horses with the C allele of the AMELY gene constituted the most ancient group. Via SNPs, CNVs, and allele-specific CNVs, much higher diversity of paternal lines can be detected than those identified with merely SNPs. Our results indicated that there are ancient paternal horse lines preserved in southwestern China, which sheds new light on the domestication and immigration of horses, and suggest that the priorities of the conservation should be given to the ancient and rare paternal lines. These three marker types provided finer phylogenetic resolution of horse patrilineal lines, and the strategies used in the present study also provide valuable reference for the genetic studies of other mammalian patrilineages.
已有报道称现代马Y染色体的核苷酸多样性极低，并且有限的Y染色体标记只能产生较差的系统发育分辨率。在本研究中，通过对来自23个中国本土马种群和4个引进马品种的300多匹雄马进行筛选，开发了三种类型的马Y染色体标记，包括单核苷酸多态性（SNP）、拷贝数变异（CNV）和等位基因特异性CNV。在约53 kb的雄性特异性Y染色体序列中发现了14个分离位点，包括AMELY基因中的一个新SNP。在14个位点中的11个检测到了CNV，同时还确定了重复片段中6个多态性位点的等位基因特异性CNV。对本研究中鉴定的SNP以及主要从欧洲马获得的先前发表的51个SNP进行系统发育分析表明，中国本土马的分化程度比欧洲和中东马深得多，而携带AMELY基因C等位基因的中国马个体构成了最古老的群体。通过SNP、CNV和等位基因特异性CNV，可以检测到比仅用SNP鉴定出的父系更高的多样性。我们的结果表明，中国西南部保存着古老的父系马系，这为马的驯化和迁移提供了新线索，并表明保护重点应放在古老和稀有的父系上。这三种标记类型为马父系谱系提供了更精细的系统发育分辨率，本研究中使用的策略也为其他哺乳动物父系遗传研究提供了有价值的参考。
