Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection
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Published:2023-09-19
Issue:1
Volume:24
Page:
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ISSN:1471-2164
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Container-title:BMC Genomics
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language:en
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Short-container-title:BMC Genomics
Author:
Shi Huibin,Li Taotao,Su Manchun,Wang Huihui,Li Qiao,Lang Xia,Ma Youji
Abstract
Abstract
Background
Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding.
Results
CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences.
Conclusions
Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.
Funder
The Education science and technology innovation project of Gansu Province The National Key R&D Program of China The Purchase contract project of the Ministry of Agriculture and Rural Affairs The Discipline Team Project of Gansu Agricultural University
Publisher
Springer Science and Business Media LLC
Subject
Genetics,Biotechnology
Reference70 articles.
1. Stranger B, Forrest M, Dunning M, Ingle C, Beazley C, Thorne N, Redon R, Bird C, de Grassi A, Lee C, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Sci (New York NY). 2007;315(5813):848–53. 2. Conrad D, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews T, Barnes C, Campbell P, et al. Origins and functional impact of copy number variation in the human genome. Nature. 2010;464(7289):704–12. 3. Chiang C, Scott A, Davis J, Tsang E, Li X, Kim Y, Hadzic T, Damani F, Ganel L, Montgomery S, et al. The impact of structural variation on human gene expression. Nat Genet. 2017;49(5):692–9. 4. Sudmant P, Mallick S, Nelson B, Hormozdiari F, Krumm N, Huddleston J, Coe B, Baker C, Nordenfelt S, Bamshad M, et al. Global diversity, population stratification, and selection of human copy-number variation. Sci (New York NY). 2015;349(6253):aab3761. 5. Luo X, Qin F, Cai G, Xiao F. Integrating genomic correlation structure improves copy number variations detection. Bioinf (Oxford England). 2021;37(3):312–7.
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