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Distribution and Functionality of Copy Number Variation across European Cattle Populations

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Date
2017
Author(s)
Upadhyay Maulik
da Silva Vinicus H
Megens Hendrik-Jan
Visker Marleen HPW
Ajmone-Marsan Paolo
Balteanu Valentin A
Dunner Susana
Garcia Jose F
Ginja Catarina
Kantanen Juha
Groenen Martien AM
Crooijmans Richard PMA
Unique identifier
10.3389/fgene.2017.00108
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Citation
Upadhyay Maulik. da Silva Vinicus H. Megens Hendrik-Jan. Visker Marleen HPW. Ajmone-Marsan Paolo. Balteanu Valentin A. Dunner Susana. Garcia Jose F. Ginja Catarina. Kantanen Juha. Groenen Martien AM. Crooijmans Richard PMA. (2017). Distribution and Functionality of Copy Number Variation across European Cattle Populations.  Frontiers in genetics, 8, 108. 10.3389/fgene.2017.00108.
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CC BY http://creativecommons.org/licenses/by/4.0/
Abstract

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.

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https://erepo.uef.fi/handle/123456789/5166
Link to the original item
http://dx.doi.org/10.3389/fgene.2017.00108
Publisher
Frontiers Media SA
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  • Luonnontieteiden ja metsätieteiden tiedekunta [1144]
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