Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data

文献类型： 外文期刊

第一作者： Qiao, Guoyan

作者： Qiao, Guoyan;Guo, Tingting;He, Xue;Yue, Yaojing;Yang, Bohui;Qiao, Guoyan;Xu, Pan

作者机构： Chinese Acad Agr Sci, Lanzhou Inst Husb & Pharmaceut Sci, Lanzhou, Peoples R China;Qinghai Commun Tech Coll, Coll Ecol Agr & Anim Husb, Xining, Peoples R China;Lanzhou Univ, Minist Agr & Rural Affairs, Coll Pastoral Agr Sci & Technol, Engn Res Ctr Grassland Ind,Minist Educ,State Key L, Lanzhou, Peoples R China

关键词： nanopore-sequencing; production traits; sheep; structural variants

期刊名称：JOURNAL OF ANIMAL BREEDING AND GENETICS （ 2022影响因子：2.6； 五年影响因子：2.4 ）

ISSN： 0931-2668

年卷期： 2024 年 141 卷 4 期

页码：

收录情况： SCI

摘要： 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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