利用全基因组长线程测序数据对一些绵羊品种的结构变异进行全基因组检测。

IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Guoyan Qiao, Pan Xu, Tingting Guo, Xue He, Yaojing Yue, Bohui Yang
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引用次数: 0

摘要

基因组结构变异(SV)在基因组遗传变异中占很大比例。长读数测序技术的快速发展为检测长片段 SVs 提供了便利。目前还没有利用羊的长片段数据检测 SV 的公开研究。我们采用长片段图谱方法检测 SV,共鉴定出 30,771 个插入、缺失、倒位和易位。我们在南道羊、高山美利奴羊、祁连白藏羊和欧拉羊中分别发现了 716、916、842 和 303 个特异性 SV。我们对这些 SV 进行了注释,发现这些 SV 相关基因主要富集在涉及免疫系统调控、生长发育和环境适应性的成熟通路中。我们根据 NGS 重测序数据检测并注释了 SV,以验证第三代检测的准确性。此外,我们还利用 PCR 方法在 50 只绵羊中验证了 5 个候选 SV。我们的研究首次使用长读数测序方法构建了绵羊的新型结构变异图谱。我们已经完成了对 SVs 对绵羊潜在影响的初步探索。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data

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.

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来源期刊
Journal of Animal Breeding and Genetics
Journal of Animal Breeding and Genetics 农林科学-奶制品与动物科学
CiteScore
5.20
自引率
3.80%
发文量
58
审稿时长
12-24 weeks
期刊介绍: The Journal of Animal Breeding and Genetics publishes original articles by international scientists on genomic selection, and any other topic related to breeding programmes, selection, quantitative genetic, genomics, diversity and evolution of domestic animals. Researchers, teachers, and the animal breeding industry will find the reports of interest. Book reviews appear in many issues.
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