Next-generation mapping of Arabidopsis genes
Next-generation mapping of Arabidopsis genes
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DOI：
10.1111/j.1365-313x.2011.04619.x
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发表时间：
2011-08-01
期刊：
影响因子：
7.2
通讯作者：
Guttman, David S.
中科院分区：
文献类型：
--
作者：
Austin, Ryan S.;Vidaurre, Danielle;Guttman, David S.
下一代基因组测序技术使通过直接测序直接绘制与感兴趣表型有关的突变成为可能。然而，迄今为止提出的大多数作图策略都需要一些事先的遗传分析，即使在遗传易驯化的生物中，这也可能非常耗时。在这里，我们提出了一种新的方法，通过对一个小的F(2)群体进行测序，快速而有力地定位EMS突变的物理位置。这种方法被称为下一代作图(NGM)，它使用贞节统计来量化亲本突变体和作图系对汇集的F(2)群体中每个SNP的相对贡献。然后，它使用这些信息根据其与突变亲本系的排他性分离来客观地定位候选突变。Http://bar.utoronto.ca/NGM.上提供了一种用户友好的、基于Web的工具，用于执行NGM分析我们使用NGM识别了与拟南芥细胞壁生物学有关的三个基因，并在功率分析中，使用少至十个F(2)系和单通道Illumina基因组分析仪数据成功地进行了测试映射。这一策略可以很容易地应用于其他模式生物，我们预计它也将在农作物和任何其他拥有完整基因组序列的真核生物中发挥作用。
Next-generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time-consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F(2) population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F(2) population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user-friendly, web-based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell-wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F(2) lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.