Zhu Caiye, Li Mingna, Qin Shizhen, Zhao Fuping, Fang Suli
College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing 100193, China.
Asian-Australas J Anim Sci. 2020 Sep;33(9):1378-1386. doi: 10.5713/ajas.18.0661. Epub 2019 Jul 1.
Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types.
In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays.
In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system.
The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.
中国本土绵羊品种按尾型可分为以下三类：脂尾羊、脂臀羊和瘦尾羊。分别对应脂尾羊、脂臀羊和瘦尾羊的典型绵羊品种是大尾寒羊、阿勒泰羊和藏羊。检测拷贝数变异（CNV）和选择信号可为不同绵羊类型表型差异的遗传机制提供信息。
在本研究中，分别使用绵羊高密度600K单核苷酸多态性芯片，运用PennCNV软件和F统计量（FST）检测三个中国本土绵羊品种X染色体上的CNV和选择信号。
在大尾寒羊、阿勒泰羊和藏羊中，分别在X染色体上鉴定出6个、4个和22个CNV区域（CNVR），长度分别为1.23 Mb、0.93 Mb和7.02 Mb。此外，在大尾寒羊、阿勒泰羊和藏羊中分别鉴定出49个、34个和55个候选选择区域，长度分别为27.49 Mb、16.47 Mb和25.42 Mb。生物信息学分析结果表明，这些区域中的几个基因与脂肪相关，包括X连锁脱氢酶/还原酶、钙电压门控通道亚基α1 F和含patatin样磷脂酶结构域4。此外，从该分析中还鉴定出其他三个基因：序列相似性家族58成员A基因与能量代谢相关，富含丝氨酸/精氨酸蛋白特异性激酶3基因与骨骼肌发育相关，白细胞介素2受体亚基γ基因与免疫系统相关。
本研究结果表明，中国本土绵羊X染色体上的CNVR和选择区域包含几个与各种遗传性状相关的基因。
