Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland.
National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
Methods Mol Biol. 2021;2222:263-286. doi: 10.1007/978-1-0716-0997-2_15.
Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The "copy-out and paste-in" life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored polymerase chain reaction (PCR) and quantitative or digital PCR with primers designed for the 5' or 3' junction. Marker systems exploiting these PCR methods can be easily developed and are inexpensively used in the absence of extensive genome sequence data. The main inter-repeat amplification polymorphism techniques include inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and Inter-Primer Binding Site (iPBS) for PCR amplification with a single or two primers.
逆转座子 (RTE) 是高度常见的移动遗传元件，由几个类别组成，构成了真核基因组的大部分。这些分散且普遍存在的 RTE 中复制转座的“复制并粘贴”生命周期导致新的基因组插入，而原始元件不会被切除。RTE 是物种多样性的重要驱动因素；它们在结构、大小和转座机制方面表现出很大的多样性，使它们成为基因组进化的重要潜在组成部分。因此，已经开发了各种应用程序来探索 RTE 插入模式的多态性。这些应用包括常规或锚定聚合酶链反应 (PCR) 和定量或数字 PCR，使用针对 5' 或 3' 接头设计的引物。利用这些 PCR 方法的标记系统可以很容易地开发，并且在没有广泛的基因组序列数据的情况下，使用成本低廉。主要的重复间扩增多态性技术包括逆转座子间扩增多态性 (IRAP)、逆转座子微卫星扩增多态性 (REMAP) 和用于单引物或双引物 PCR 扩增的引物结合位点 (iPBS)。
