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Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

文献类型： 外文期刊

作者： Zhang, Yaran 1 ; Hu, Yan 2 ; Wang, Xiuge 1 ; Jiang, Qiang 1 ; Zhao, Han 1 ; Wang, Jinpeng 1 ; Ju, Zhihua 1 ; Yang, Liguo 2 ; Gao, Yaping 1 ; Wei, Xiaochao 1 ; Bai, Jiachen 1 ; Zhou, Yang 2 ; Huang, Jinming 1 ;

作者机构： 1.Shandong Acad Agr Sci, Dairy Cattle Res Ctr, Jinan, Peoples R China

2.Huazhong Agr Univ, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan, Peoples R China

3.Huazhong Agr Univ, Coll Anim Sci & Technol, Wuhan, Peoples R China

4.Engn Ctr Anim Breeding & Reprod, Jinan, Peoples R China

关键词： copy number variations; Chinese cattle; population structure; selection signatures; high-altitude adaptation

期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）

ISSN：

年卷期： 2020 年 10 卷

页码：

收录情况： SCI

摘要： Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp-4,477,860 bp in size), covering 14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurusxBos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

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[1]Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle. Zhang, Yaran,Wang, Xiuge,Jiang, Qiang,Zhao, Han,Wang, Jinpeng,Ju, Zhihua,Gao, Yaping,Wei, Xiaochao,Bai, Jiachen,Huang, Jinming,Hu, Yan,Yang, Liguo,Zhou, Yang,Hu, Yan,Yang, Liguo,Zhou, Yang,Huang, Jinming. 2020

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