Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China.
College of Ecological Agriculture and Animal Husbandry, Qinghai Communications Technical College, Xining, China.
J Anim Breed Genet. 2024 Jul;141(4):403-414. doi: 10.1111/jbg.12846. Epub 2024 Jan 21.
Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long-reads sequencing has facilitated the detection of long-fragment SVs. There is no published study to detect SVs using long-read data from sheep. We applied a long-read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions and translocations. We identified 716, 916, 842 and 303 specific SVs in Southdown sheep, Alpine merino sheep, Qilian White Tibetan sheep and Oula sheep, respectively. We annotated these SVs and found that these SV-related genes were primarily enriched in the well-established pathways involved in the regulation of the immune system, growth and development and environmental adaptability. We detected and annotated SVs based on NGS resequencing data to validate the accuracy based on third-generation detection. Moreover, five candidate SVs were verified using the PCR method in 50 sheep. Our study is the first to use a long-reads sequencing approach to construct a novel structural variation map in sheep. We have completed a preliminary exploration of the potential effects of SVs on sheep.
基因组结构变异（SVs）构成了基因组遗传变异的重要部分。长读长测序的快速发展促进了长片段 SVs 的检测。目前还没有使用绵羊长读长数据检测 SVs 的发表研究。我们应用长读长映射方法来检测 SVs，并对总共 30771 个插入、缺失、倒位和易位进行了特征描述。我们分别在萨福克羊、阿尔卑斯美利奴羊、祁连白藏羊和欧拉羊中鉴定出了 716、916、842 和 303 个特定的 SVs。我们对这些 SVs 进行了注释，发现这些与 SV 相关的基因主要富集在已建立的与免疫系统调节、生长发育和环境适应性相关的途径中。我们基于 NGS 重测序数据检测和注释了 SVs，以基于第三代检测来验证准确性。此外，我们在 50 只绵羊中使用 PCR 方法验证了 5 个候选 SVs。本研究首次使用长读长测序方法构建了绵羊的新型结构变异图谱。我们已经对 SVs 对绵羊的潜在影响进行了初步探索。
