文献类型： 外文期刊

作者： Xia, Xiaoting ¹ ; Zhang, Fengwei ¹ ; Li, Shuang ¹ ; Luo, Xiaoyu ¹ ; Peng, Lixin ² ; Dong, Zheng ¹ ; Pausch, Hubert ³ ; Leonard, Alexander S. ³ ; Crysnanto, Danang ³ ; Wang, Shikang ¹ ; Tong, Bin ⁴ ; Lenstra, Johannes A. ⁵ ; Han, Jianlin ⁶ ; Li, Fuyong ⁸ ; Xu, Tieshan ⁹ ; Gu, Lihong ¹⁰ ; Jin, Liangliang ¹ ; Dang, Ruihua ¹ ; Huang, Yongzhen ¹ ; Lan, Xianyong ¹ ; Ren, Gang ¹ ; Wang, Yu ¹ ; Gao, Yuanpeng ¹¹ ; Ma, Zhijie ¹² ; Cheng, Haijian ¹ ; Ma, Yun ¹⁴ ; Chen, Hong ¹ ; Pang, Weijun ¹ ; Lei, Chuzhao ¹ ; Chen, Ningbo ¹ ;

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

2.Guangxi Acad Sci, Natl Engn Res Ctr Nonfood Biorefinery, 98 Daling Rd, Nanning, Peoples R China

3.Swiss Fed Inst Technol, Anim Genom, Univ Str 2, CH-8006 Zurich, Switzerland

4.Inner Mongolia Univ, Sch Life Sci, State Key Lab Reprod Regulat & Breeding Grassland, Hohhot, Peoples R China

5.Univ Utrecht, Fac Vet Med, Utrecht, Netherlands

6.Int Livestock Res Inst ILRI, Livestock Genet Program, Nairobi, Kenya

7.Chinese Acad Agr Sci CAAS, Inst Anim Sci, CAAS ILRI Joint Lab Livestock & Forage Genet Resou, Beijing, Peoples R China

8.City Univ Hong Kong, Jockey Club Coll Vet Med & Life Sci, Dept Infect Dis & Publ Hlth, Hong Kong, Peoples R China

9.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Haikou, Peoples R China

10.Hainan Acad Agr Sci, Inst Anim Sci & Vet Med, Haikou, Peoples R China

11.Northwest A&F Univ, Coll Vet Med, Xianyang, Yangling, Peoples R China

12.Qinghai Univ, Qinghai Acad Anim Sci & Vet Med, Xining, Peoples R China

13.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Shandong Key Lab Anim Dis Control & Breeding, Jinan, Peoples R China

14.Ningxia Univ, Sch Agr, Key Lab Ruminant Mol & Cellular Breeding Ningxia H, Yinchuan, Peoples R China

关键词： Structural variation; Genome assembly; Long-read sequencing; East Asian cattle

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundStructural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle.ResultsIn this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle.ConclusionsOur findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.