文献类型： 外文期刊

作者： Li, Ran ¹ ; Gong, Mian ¹ ; Zhang, Xinmiao ¹ ; Wang, Fei ¹ ; Liu, Zhenyu ¹ ; Zhang, Lei ¹ ; Yang, Qimeng ¹ ; Xu, Yuan ¹ ; Xu, Mengsi ² ; Zhang, Huanhuan ¹ ; Zhang, Yunfeng ² ; Dai, Xuelei ¹ ; Gao, Yuanpeng ¹ ; Zhang, Zhuangbiao ¹ ; Fang, Wenwen ¹ ; Yang, Yuta ¹ ; Fu, Weiwei ¹ ; Cao, Chunna ¹ ; Yang, Peng ² ; Ghanatsaman, Zeinab Amiri ³ ; Negari, Niloufar Jafarpour ⁴ ; Nanaei, Hojjat Asadollahpour ⁵ ; Yue, Xiangpeng ⁶ ; Song, Yuxuan ¹ ; Lan, Xianyong ¹ ; Deng, Weidong ⁷ ; Wang, Xihong ¹ ; Pan, Chuanying ¹ ; Xiang, Ruidong ⁸ ; Ibeagha-Awemu, Eveline M. ⁹ ; Heslop-Harrison, Pat (J. S. ) ¹⁰ ; Rosen, Benjamin D. ¹¹ ; Lenstra, Johannes A. ¹² ; Gan, Shangquan ² ; Jiang, Yu ¹ ;

作者机构： 1.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Shaanxi, Peoples R China

2.Xinjiang Acad Agr & Reclamat Sci, State Key Lab Sheep Genet Improvement & Healthy P, Shihezi 832000, Xinjiang, Peoples R China

3.Agr Res Educ & Extens Org AREEO, Fars Agr & Nat Resources Res & Educ Ctr, Dept Anim Sci, Shiraz 7155863511, Iran

4.Shahid Bahonar Univ Kerman, Dept Anim Sci, Kerman 7616914111, Iran

5.Avicenna Res Inst, Reprod Biotechnol Res Ctr, ACECR, Tehran 1983969412, Iran

6.Lanzhou Univ, Coll Pastoral Agr Sci & Technol,State Key Lab Gra, Minist Educ,Key Lab Grassland Livestock Ind Innov, Minist Agr & Rural Affairs,Engn Res Ctr Grassland, Lanzhou 730020, Peoples R China

7.Yunnan Agr Univ, Fac Anim Sci & Technol, Kunming 650201, Yunnan, Peoples R China

8.Univ Melbourne, Fac Vet & Agr Sci, Parkville, Vic, Australia

9.Agr & Agri Food Canada, Sherbrooke Res & Dev Ctr, Sherbrooke, PQ J1M 0C8, Canada

10.Univ Leicester, Dept Genet & Genome Biol, Leicester LE1 7RH, Leics, England

11.USDA ARS, Anim Genom & Improvement Lab, Beltsville, MD 20705 USA

12.Univ Utrecht, Fac Vet Med, NL-3508 TD Utrecht, Netherlands

13.Guangdong Ocean Univ, Coll Coastal Agr Sci, Zhanjiang 524088, Peoples R China

14.Northwest A&F Univ, Key Lab Livestock Biol, Yangling 712100, Shaanxi, Peoples R China

期刊名称：GENOME RESEARCH （ 影响因子：7.0； 五年影响因子：11.8 ）

ISSN： 1088-9051

年卷期： 2023 年 33 卷 3 期

页码：

收录情况： SCI

摘要： Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5 ' untranslated region (5 ' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.