Data from: Distribution and functionality of copy number variation across European cattle populations

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 colour-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.

拷贝数变异（Copy number variation, CNV）以DNA片段的大规模缺失与扩增为主要特征，对遗传与表型变异具有显著贡献。对不同欧洲牛群体的拷贝数变异进行解析，或可揭示介导表型差异的遗传改变；此类改变在牛的驯化历程中，由作用于种群的进化压力持续累积形成。为探究欧洲牛群体的拷贝数变异分布模式，本研究利用因美纳（Illumina）牛高密度基因分型芯片，对代表欧洲不同区域的149份个体样本进行基因分型。本研究采用隐马尔可夫模型（Hidden Markov Model, HMM）并依托PennCNV软件，在149份样本中总计鉴定得到9944个常染色体拷贝数变异。源自不列颠群岛多个品种、巴尔干半岛及意大利区域的牛只，其平均拷贝数变异检出量显著高于荷兰牛与阿尔卑斯牛群体。通过整合至少两份样本重叠的拷贝数变异，本研究共鉴定得到923个拷贝数变异区域（CNV regions, CNVRs）。对鉴定得到的拷贝数变异区域进行层级聚类分析后发现，欧洲牛群体间的遗传分化程度较低，且存在高频拷贝数变异区域的共享现象。本研究鉴定的多个拷贝数变异区域，与嗅觉受体基因及免疫相关基因存在基因组位置上的重叠。此外，本研究还在英国长角牛群体中检测到一处覆盖Kit基因的拷贝数变异；该Kit基因此前已被证实与牛的色边被毛性状相关。综上，本研究对欧洲牛基因组内拷贝数变异的分布情况进行了全面概述。研究结果显示，纯化选择与基因组漂变在塑造不同欧洲牛群体间的拷贝数变异多样性过程中扮演了关键角色。