Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing
Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing
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DOI：
10.2144/000113084
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发表时间：
2009-03-01
期刊：
影响因子：
2.7
通讯作者：
Gemmell, Neil J.
中科院分区：
文献类型：
--
作者：
Abdelkrim, Jawad;Robertson, Bruce C.;Gemmell, Neil J.
微卫星是许多群体遗传学研究的首选遗传标记，但在缺乏先前遗传数据的情况下，必须使用重组方法从头分离。在这里，我们利用高通量基因组测序技术来产生数百万个碱基对的短片段读段，这些读段用生物信息学工具集进行筛选，以确定扩增多态性微卫星位点的引物。使用这种方法，我们分离出13个多态性微卫星的蓝鸭（Hymenolaimus malacorhynchos），一个物种，有限的遗传数据。我们的基因组方法消除了重组遗传步骤，与传统方法相比，显著降低了标记开发的时间和成本要求。虽然基因组测序的这种应用对许多人来说似乎是显而易见的，但据我们所知，这项研究是第一次尝试描述使用基因组测序在非模式生物或任何生物中开发微卫星标记。
Microsatellites are the genetic markers of choice for many population genetic Studies, but must be isolated de novo using recombinant approaches where prior genetic data are lacking. Here we utilized high-throughput genomic sequencing technology to produce millions of base pairs of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci. Using this approach we isolated 13 polymorphic microsatellites for the blue duck (Hymenolaimus malacorhynchos), a species for which limited genetic data were available. Our genomic approach eliminates recombinant genetic steps, significantly reducing the time and cost requirements of marker development compared with traditional approaches. While this application of genomic sequencing may seem obvious to many, this study is, to the best of our knowledge, the first attempt to describe the use of genomic sequencing for the development of microsatellite markers in a non-model organism or indeed any organism.