Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
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DOI：
10.1371/journal.pone.0003376
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发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Johnson EA
中科院分区：
文献类型：
--
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
单核苷酸多态(SNP)的发现和基因分型是遗传图谱的关键。仍然需要一种简单、廉价的平台，允许在大量人群中进行高密度SNP发现和基因分型。在这里，我们描述了限制位点相关DNA(RAD)标签的测序，它识别了超过13,000个SNP，并在两个模式生物中定位了三个特征，使用的容量不到一次Illumina测序的一半。我们证明，选择不同的限制性内切酶可以获得不同的标记密度。此外，我们还开发了一个用于样本多重分析的条形码系统，并通过鉴定F2代个体中的重组断裂点，精细定位了三刺鱼侧板盔甲丢失的遗传基础。条形码还通过对个体进行电子重新排序，促进了第二个特征的映射，即减少骨盆结构。为了进一步证明RAD测序方法的简便性，我们确定了多态标记，并定位了粗糙脉孢菌的一个诱导突变。RAD标记测序是SNP发现和基因分型的综合平台。这种方法应该广泛适用于各种生物体的遗传作图。
Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.
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影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
通讯作者：
Johnson, Eric A.
影响因子：
4.4
作者：
Coyne, KJ;Burkholder, JM;Cary, SC
通讯作者：
Cary, SC
影响因子：
48
作者：
Lai, Chao-Qiang;Leips, Jeff;Mackay, Trudy F. C.
通讯作者：
Mackay, Trudy F. C.
DOI：
10.1073/pnas.0401076101
发表时间：
2004-06-29
影响因子：
11.1
作者：
Wenzl, P;Carling, J;Kilian, A
通讯作者：
Kilian, A
影响因子：
64.8
作者：
Shapiro, MD;Marks, ME;Kingsley, DM
通讯作者：
Kingsley, DM