Yuan Chao, Lu Zengkui, Guo Tingting, Yue Yaojing, Wang Xijun, Wang Tianxiang, Zhang Yajun, Hou Fujun, Niu Chune, Sun Xiaopin, Zhao Hongchang, Zhu Shaohua, Liu Jianbin, Yang Bohui
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China.
BMC Genomics. 2021 Jan 23;22(1):78. doi: 10.1186/s12864-021-07387-7.
Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.
A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. "Deletion" events took place more frequently than "duplication" or "both" events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39-55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection.
In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.
拷贝数变异（CNV）是遗传变异的重要来源，对表型多样性、经济重要性状以及家畜物种的进化具有重大影响。在本研究中，利用重测序技术分析了三个品种的32只细毛羊的全基因组CNV分布特征。
本研究共检测到1,747,604个CNV，合并重叠的CNV后获得7228个CNV区域（CNVR）；这些区域占绵羊参考基因组的2.17%。CNVR的平均长度为4307.17 bp。“缺失”事件比“重复”或“两者皆有”事件发生得更频繁。获得的CNVR与先前报道的绵羊CNVR在不同程度上重叠（4.39 - 55.46%）。功能富集分析表明，含有CNVR的基因主要参与感觉系统、营养代谢过程以及生长发育过程。此外，1855个CNVR与166个数量性状位点（QTL）相关，包括产奶QTL、胴体QTL以及与健康相关的QTL等。另外，将32只细毛羊分为有角和无角两组，分析CNVR的选择性清除，发现松弛素家族肽受体2（RXFP2）基因受到强烈的选择影响。
总之，我们利用重测序构建了中国本土细毛羊的基因组CNV图谱，从而为绵羊基因组研究提供了宝贵的遗传变异资源，这将有助于绵羊复杂性状的研究。
