Shin Wonseok, Kim Haneul, Oh Dong-Yep, Kim Dong Hee, Han Kyudong
Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.
Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
Genomics Inform. 2020 Mar;18(1):e4. doi: 10.5808/GI.2020.18.1.e4. Epub 2020 Mar 31.
Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.
转座元件（TEs）约占牛基因组的一半。在基因组进化时，通过结构变异（SV），它们可以成为强大的物种特异性标记，且不会发生回复突变。在之前的一项研究中，我们使用传统PCR方法和桑格测序验证，鉴定出了由TE关联缺失事件产生的韩牛特异性SV。它可以用作区分不同牛品种（即韩牛与荷斯坦牛）的分子标记。然而，PCR对于每个样本的各种最终拷贝定量存在缺陷。因此，我们应用液滴数字PCR（ddPCR）平台对韩牛特异性SV进行精确的定量检测。尽管韩牛群体内样本的等位基因频率变化较低，但ddPCR可以通过绝对定量进行高灵敏度检测。我们旨在使用ddPCR实现比PCR更精确的定量。我们认为ddPCR平台适用于分子标记的定量评估。
