奶山羊是最早的奶牛畜种之一,在经济发展中发挥着重要作用,特别是对于发展中国家。随着农业文明的发展,奶山羊已广泛分布在世界各地。然而,关于奶山羊的具体特性的研究很少。在这项研究中,我们通过对48只山羊进行测序和使用41只公开可用的山羊,收集了89只山羊的全基因组数据,包括五个奶山羊品种(Saanen,努比亚人,高山,Toggenburg,和关中奶山羊;n=24、15、11、6、6),和三个山羊品种(龟山山羊,隆林山羊,云上黑山羊;n=6,15,6)。通过比较奶山羊和非奶山羊的基因组,分析奶山羊的遗传多样性和选择特征。结果表明,八只山羊可以分为三个欧洲亚组,非洲,和中国本地山羊种群,我们还发现澳大利亚努比亚人,Toggenburg,澳大利亚阿尔卑斯山的连锁不平衡最高,核苷酸多样性的最低水平,和更高的近亲繁殖系数,表明它们是人为选择的。此外,我们确定了几个与奶山羊特异性相关的候选基因,特别是与产奶性状相关的基因(GHR,DGAT2,ELF5,GLYCAM1,ACSBG2,ACSS2),繁殖性状(TSHR,TSHB,PTGS2,ESR2),免疫性状(JAK1、POU2F2、LRRC66)。我们的结果不仅为奶山羊的进化史和品种特征提供了见解,同时也为奶山羊杂交育种方案的实施和完善提供了有价值的信息。
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.