Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
College of Animal Science and Technology, Shaanxi Key Laboratory of Agricultural Molecular Biology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Heredity (Edinb). 2019 May;122(5):636-646. doi: 10.1038/s41437-018-0150-6. Epub 2018 Nov 6.
Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.
山羊（Capra hircus）是一种重要的农场动物物种。拷贝数变异（CNV）代表了基因组结构变异的主要来源。我们使用 ADAPTmap 项目生成的 CaprineSNP50 基因分型数据研究了山羊中 CNV 分布的多样性。我们使用 PennCNV 在来自 50 个山羊品种的 1023 个样本中鉴定了 6286 个推定的 CNV。这些 CNV 合并为 978 个 CNV 区域，跨越约 262Mb 的总长度，对应于山羊基因组的约 8.96%。然后，我们根据地理分布将样本分为六个亚组，并构建了比较 CNV 图谱。我们的结果显示，不同地理区域的 CNV 存在种群分化，包括西亚、东地中海、阿尔卑斯山和北欧、马达加斯加、西北非和东南非群体。基于不同群体中每个个体的 CNV 计数进行聚类热图分析的结果与基于 SNP 数据生成的结果大致一致，这可能反映了不同山羊品种的种群历史。我们试图确定这些 CNV 事件的基因内容，发现了几个重要的 CNV 重叠基因（例如 EDNRA、ADAMTS20、ASIP、KDM5B、ADAM8、DGAT1、CHRNB1、CLCN7 和 EXOSC4），这些基因参与了毛色、肌肉发育、代谢过程、骨硬化症和胚胎发育等局部适应。因此，这项研究在全球山羊群体中生成了广泛的 CNV 图谱，为山羊基因组及其功能注释提供了新的见解。
