Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
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DOI：
10.1101/gr.5681207
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发表时间：
2007-02-01
期刊：
影响因子：
7
通讯作者：
Johnson, Eric A.
中科院分区：
文献类型：
--
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
限制性位点相关DNA（RAD）标签是通过短DNA标签在全基因组范围内表示特定限制性酶的每个位点。大多数生物分离大量的DNA序列多态性，破坏限制性位点，这使得RAD标签作为遗传标记，以高密度分布在整个基因组中。在这里，我们证明了RAD标记的适用性，为个人和批量分离基因分型。首先，我们表明，这些标志物可以识别和预先存在的微阵列格式类型。其次，我们提出了一种方法，使用RAD标记DNA快速产生一个低成本的微阵列基因分型资源，可用于有效地识别和类型的RAD标记数千。我们证明了前一种方法的实用性，通过使用平铺路径阵列的果蝇映射重组断点，和后一种方法通过创建和使用一个丰富的RAD标记阵列的threespine刺鱼。大量的RAD标志物能够定位先前鉴定的区域，以及也与侧板表型相关的第二区域。两者合计，我们的研究结果表明，RAD标记，并开发RAD标记微阵列资源的方法，允许在模型和非模型系统的高通量，高分辨率基因分型。
Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.