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 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.

拷贝数变异（Copy Number Variation, CNV）以DNA片段的大规模缺失或扩增为典型特征，对遗传与表型变异具有显著贡献。对不同欧洲牛种群的拷贝数变异进行评估，或可揭示导致表型差异的遗传变异——这类变异是牛驯化历史中，受进化压力作用而累积形成的。为探究欧洲牛群体的拷贝数变异模式，本研究使用Illumina牛高密度基因分型芯片（Illumina Bovine HD Genotyping array），对代表欧洲不同地区的149份个体样本进行基因分型。借助PennCNV工具所采用的隐马尔可夫模型（Hidden Markov Model, HMM），本研究在149份样本中共计鉴定出9944条常染色体拷贝数变异。来自不列颠群岛多个品种、巴尔干与意大利地区的牛群，其平均拷贝数变异数量高于荷兰牛群或阿尔卑斯牛群。通过整合至少两份样本中共有的拷贝数变异，本研究共计鉴定出923个拷贝数变异区域（CNV Regions, CNVRs）。对拷贝数变异区域进行层级聚类分析的结果显示，欧洲牛种群间的分化程度较低，且存在大量高频共享的拷贝数变异区域。本研究鉴定出的多个拷贝数变异区域与嗅觉受体基因及免疫系统相关基因存在重叠。此外，本研究在英国长角牛（English Longhorn cattle）中检测到一处与Kit基因重叠的拷贝数变异，该变异此前已被证实与边花毛色性状相关。综上，本研究全面解析了欧洲牛基因组中的拷贝数变异分布情况。研究结果表明，纯化选择与基因组漂变在塑造不同欧洲牛种群间的拷贝数变异多样性方面发挥了重要作用。