Advances in plant gene-targeted and functional markers: a review.
Advances in plant gene-targeted and functional markers: a review.
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DOI：
10.1186/1746-4811-9-6
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发表时间：
2013-02-13
期刊：
影响因子：
5.1
通讯作者：
Hyvönen J
中科院分区：
文献类型：
--
作者：
Poczai P;Varga I;Laos M;Cseh A;Bell N;Valkonen JP;Hyvönen J
公共基因组数据库为分子标记的发展提供了新的方向，并引发了植物科学中常用的基于聚合酶链式反应的技术类型的转变。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公认的任意扩增DNA方法的实践，但采用了新的方法学创新，如在引物中加入基因或启动子元件。这些标记通过同时出现显性和共显性条带，提供了良好的重复性和更高的分辨率。尽管这些半随机标记有很好的特点，但它们可能存在碰撞和非同源性问题，类似于随机生成的指纹。植物基因组中大量存在的转座子也可以用来产生指纹。这些标记通过利用特定的靶点提供更大的基因组覆盖率，并产生似乎大多是同源的条带。大多数这些技术的最大缺点是需要关于反转录转座子的事先基因组信息来设计引物，这阻碍了普遍应用。另一类最近开发的方法利用存在于多拷贝基因家族(如细胞色素P450和β-微管蛋白基因)中的长度多态性来提供跨物种扩增和可转移性。一类特定的标记利用植物抗性基因的共同特征来产生与给定表型相关联的条带，或揭示遗传多样性。保守的基于DNA的策略基因组覆盖有限，可能无法揭示遗传多样性，而抗性基因可能处于特定的进化选择之下。也可以使用不同的基因定位方法，结合使用RNA信息，从基因组的功能和/或转录区域产生标记。这种技术有可能产生表型连锁的功能标记，特别是当指纹是从基因组的转录或表达区域产生的时候。可以预料的是，这些最近开发的技术将产生更大的数据集，但也应该承认和仔细调查它们的缺点。
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.
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影响因子：
3.1
作者：
Breviario, Diego;Baird, Wm. Vance;Giani, Silvia
通讯作者：
Giani, Silvia
影响因子：
7.2
作者：
Alonso-Blanco, C;Peeters, AJM;Kuiper, MTR
通讯作者：
Kuiper, MTR
影响因子：
3
作者：
Archibald, Jenny K.;Crawford, Daniel J.;Mort, Mark E.
通讯作者：
Mort, Mark E.
影响因子：
7.2
作者：
Bachem, CWB;vanderHoeven, RS;Visser, RGF
通讯作者：
Visser, RGF
影响因子：
7.2
作者：
Brugmans, B;del Carmen, AF;Visser, RGF
通讯作者：
Visser, RGF