Shi Rui, Zhang Yi, Wang Ya Chun, Huang Tao, Lu Guo Chang, Yue Tao, Lu Zhen Xi, Huang Xi Xia, Wei Xin Pu, Feng Shu Tang, Chen Jun, Kagedeer Wu Lan, Abulizi Ruxianguli, Muhetaer Nuerhumaer
Key Laboratory of Animal Genetics, Breeding and Reproduction(MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
College of Animal Science and Technology, Xinjiang Shihezi University, Shihezi 832000, China.
Yi Chuan. 2020 May 20;42(5):493-505. doi: 10.16288/j.yczz.20-071.
Xinjiang inbred cattle is a population which has been highly inbred for 45 years. However, the breed origin of this population cannot be traced back due to the lack of original records. To demonstrate the genetic background of Xinjiang inbred cattle, we analysed the worldwide genomic information of 16 cattle breeds using principal components analysis, and Admixture method. Furthermore, the shared SNP markers of Xinjiang inbred cattle, local Kazakh cattle, Holstein cattle, and Xinjiang Brown cattle were extracted to calculate population genetic parameters and genomic inbreeding indicators in order to evaluate the magnitude of inbreeding in each population. We also evaluated the relationship between inbreeding indicators and body size in the Xinjiang inbred population. Finally, the high frequency runs of homozygosity (ROH) regions for Xinjiang inbred cattle and local Kazakh population were selected for genes and QTL annotations. These results demonstrate that the ancestry proportions of inbreeding breed are similar to those of Kazakh cattle. The genomic homozygosity of Xinjiang inbred cattle is significantly higher than other populations; the inbreeding depression is observed in body size to a certain extent because body size decreased when corresponding homozygosity increased. Totally, six basic bio-pathways and 32 QTL regions that related to bovine economical traits were annotated. Our results provide the insights into breeding strategies, future protection, and utilization plan design for this special genetic material-Xinjiang inbred cattle.
新疆近交牛是一个已经高度近交45年的群体。然而，由于缺乏原始记录，该群体的品种起源无法追溯。为了阐明新疆近交牛的遗传背景，我们使用主成分分析和Admixture方法分析了16个牛品种的全球基因组信息。此外，提取了新疆近交牛、当地哈萨克牛、荷斯坦牛和新疆褐牛的共享单核苷酸多态性（SNP）标记，以计算群体遗传参数和基因组近交指标，从而评估每个群体的近交程度。我们还评估了新疆近交群体中近交指标与体尺之间的关系。最后，选择了新疆近交牛和当地哈萨克群体的高频纯合片段（ROH）区域进行基因和数量性状基因座（QTL）注释。这些结果表明，近交品种的祖先比例与哈萨克牛相似。新疆近交牛的基因组纯合度显著高于其他群体；在一定程度上观察到体尺存在近交衰退现象，因为随着相应纯合度的增加，体尺减小。总共注释了6条与牛经济性状相关的基本生物途径和32个QTL区域。我们的研究结果为这种特殊遗传材料——新疆近交牛的育种策略、未来保护和利用计划设计提供了见解。
