A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle
A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle
复制标题
使用高密度单核苷酸多态性阵列对西门塔尔牛进行全基因组拷贝数变异扫描
DOI：
10.1111/age.12288
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发表时间：
2015
期刊：
影响因子：
2.4
通讯作者：
Ren Hongyan
中科院分区：
文献类型：
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作者：
Wu Yang;Fan Huizhong;Jing Shengyun;Xia Jiangwei;Chen Yan;Zhang Lupei;Gao Xue;Li Junya;Gao Huijiang;Ren Hongyan
拷贝数变异（CNVs）最近被确定为有希望的遗传变异来源，与单核苷酸多态性（snp）互补。因此，CNVs的检测引起了人们的广泛关注。在这项研究中，我们使用Illumina牛HD BeadChip （770k）数据对792头西门塔牛进行全基因组CNV检测。共鉴定出263个CNVRs，其中损失区137个，增益区102个，增益区24个，覆盖牛基因组35.48 Mb（1.41%）。CNVRs的长度范围为10.18 ~ 1.76 Mb，平均长度为134.78 kb，中位数长度为61.95 kb。在其中的136个区域中，共鉴定出313个与跨膜活性和嗅觉转导活性等生物学功能相关的基因。为了验证结果，我们对随机选择的9个cnvr进行了定量PCR检测，成功确认了7个（77.6%）。我们的研究结果提出了一个来自高密度SNP数据的牛CNV图谱，它扩展了目前牛基因组的CNV图谱，并为牛基因组结构变异的研究提供了有用的信息。
Copy number variations (CNVs) have recently been identified as promising sources of genetic variation, complementary to single nucleotide polymorphisms (SNPs). As a result, detection of CNVs has attracted a great deal of attention. In this study, we performed genome‐wide CNV detection using Illumina Bovine HD BeadChip (770k) data on 792 Simmental cattle. A total of 263 CNV regions (CNVRs) were identified, which included 137 losses, 102 gains and 24 regions classified as both loss and gain, covering 35.48 Mb (1.41%) of the bovine genome. The length of these CNVRs ranged from 10.18 kb to 1.76 Mb, with an average length of 134.78 kb and a median length of 61.95 kb. In 136 of these regions, a total of 313 genes were identified related to biological functions such as transmembrane activity and olfactory transduction activity. To validate the results, we performed quantitative PCR to detect nine randomly selected CNVRs and successfully confirmed seven (77.6%) of them. Our results present a map of cattle CNVs derived from high‐density SNP data, which expands the current CNV map of the cattle genome and provides useful information for investigation of genomic structural variation in cattle.