Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland.
Plant Methods. 2013 Feb 13;9(1):6. doi: 10.1186/1746-4811-9-6.
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.
公共基因组数据库为分子标记的开发提供了新的方向，并引发了植物科学中常用的基于 PCR 的技术类型的转变。除了常用的任意扩增 DNA 标记外，还开发了其他方法。靶向指纹标记技术基于任意扩增 DNA 方法的成熟实践，但采用了新的方法学创新，例如在引物中纳入基因或启动子元件。这些标记物通过显性和共显性带的并发出现提供了良好的可重复性和更高的分辨率。尽管这些半随机标记物具有很有前景的特征，但它们可能会遇到与随机生成的指纹一样的碰撞和非同源性问题。转座元件在植物基因组中大量存在，也可用于生成指纹。这些标记物通过利用特定的靶向位点提供了更高的基因组覆盖，并产生了大多数似乎是同源的带。这些技术的最大缺点是，引物设计需要关于逆转座子的先前基因组信息，这限制了它们的普遍应用。最近开发的另一种方法类利用多拷贝基因家族（如细胞色素 P450 和 β-微管蛋白基因）阵列中存在的长度多态性，提供跨物种扩增和可转移性。一类特定的标记物利用植物抗性基因的共同特征来产生与给定表型相关的带，或揭示遗传多样性。基于保守 DNA 的策略的基因组覆盖有限，可能无法揭示遗传多样性，而抗性基因可能受到特定的进化选择。标记也可以使用不同的基因靶向方法从基因组的功能和/或转录区生成，并结合使用 RNA 信息。这些技术有可能生成与表型相关的功能性标记物，特别是当指纹是从基因组的转录或表达区域生成时。预计这些最近开发的技术将产生更大的数据集，但也应该承认并仔细研究它们的缺点。
