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Series GSE142218 Query DataSets for GSE142218
Status Public on Feb 21, 2020
Title Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle
Platform organism Bos taurus
Sample organisms Bos taurus; Bos indicus; Bos grunniens
Experiment type Genome variation profiling by SNP array
Summary 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 taurus×Bos 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.
 
Overall design We initially genotyped 375 individuals representing 25 Chinese indigenous cattle breeds, as well as 39 individuals representing two yak breeds as outgroups. After quality control filtering for chip data, a total of 355 individuals including 318 Chinese indigenous cattle and 37 yaks (outgroups in our study) were retained and used for further analyses. We detected their genome-wide CNVs, and analyzed their population structure based on these CNVs. We used the pairwise Fst method to explore the selection signatures of CNVs positively involved in high-altitude adaptation, by comparing cattle breeds native to high-altitude plateau with those native to low-altitude land within taurine-type breeds and within Bos taurus×Bos indicus hybrids, respectively.
Web link https://www.frontiersin.org/articles/10.3389/fgene.2019.01404/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_1250403_30_Geneti_20200220_arts_A
 
Contributor(s) Zhang Y, Hu Y, Wang X, Jiang Q, Zhao H, Wang J, Ju Z, Yang L, Gao Y, Wei X, Bai J, Zhou Y, Huang J
Citation(s) 32117428
Front. Genet., 14 February 2020 | https://doi.org/10.3389/fgene.2019.01404
Submission date Dec 17, 2019
Last update date Nov 08, 2022
Contact name Yaran Zhang
E-mail(s) zhang_ya_ran@126.com
Phone 18853115768
Organization name Shandong Acdemy of Agricultural Sciences
Street address North industrial road
City Ji'nan
ZIP/Postal code 250100
Country China
 
Platforms (1)
GPL21267 BovineHD BeadChip
Samples (355)
GSM4222932 Whole blood, ALT01
GSM4222933 Whole blood, ALT02
GSM4222934 Whole blood, ALT03
Relations
BioProject PRJNA596234

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE142218_RAW.tar 3.6 Gb (http)(custom) TAR (of IDAT)
GSE142218_matrix.txt.gz 2.1 Gb (ftp)(http) TXT
Processed data are available on Series record
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