National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
BMC Genomics. 2013 Apr 8;14:229. doi: 10.1186/1471-2164-14-229.
In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.
Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.
In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.
近年来，全基因组关联研究成功揭示了与疾病和数量表型等复杂特征相关的单核苷酸多态性（SNP）。这些变异仅占遗传力的一小部分。随着高通量技术的发展，在生物体中发现了大量的亚微观结构变异，其中主要的变异是拷贝数变异（CNV）。因此，CNV 越来越被认为是遗传变异和表型多样性的重要和丰富来源。
使用绵羊 SNP50 BeadChip 阵列分析了三个绵羊品种的基因组中的 CNV。共鉴定出 238 个 CNV 区域（CNVR），包括 219 个缺失、13 个增益和 6 个同时发生（缺失和增益），这些区域覆盖了绵羊基因组序列的 60.35 Mb，对应于常染色体基因组序列的 2.27%。常染色体上的 CNVR 长度从 13.66 kb 到 1.30 Mb 不等，平均大小为 253.57 kb，75 个 CNVR 事件的频率>3%。这些 CNVR 中，通过 PennCNV 鉴定的 47 个 CNVR 与 CNVpartition 重叠。功能分析表明，CNVR 中的大多数基因都显著富集于环境响应。此外，选择了 10 个 CNVR 进行验证，并通过 qPCR 进一步实验验证了 6 个 CNVR。此外，在我们的新数据集和其他已发表的反刍动物 CNV 研究中，有 57 个 CNVR 重叠。
在这项研究中，我们首次基于 Ovine SNP50 阵列构建了绵羊 CNV 图谱。我们的结果表明，两种检测工具的差异以及多种算法的整合可以增强绵羊基因组结构变异的检测。此外，我们的研究结果将有助于了解绵羊基因组，并为未来开展与绵羊重要经济表型相关的 CNVs 关联研究提供初步基础。
