Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy
Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy
复制标题
使用基于纳米孔的测序策略绘制大豆转基因等位基因图谱。
DOI：
10.1093/jxb/erz202
复制
发表时间：
2019-08-01
影响因子：
6.9
通讯作者：
Yu, Bin
中科院分区：
文献类型：
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作者：
Li, Shengjun;Jia, Shangang;Yu, Bin
40年前，转基因技术被开发出来，将转基因引入各种生物中，以验证基因功能并增加遗传变异。然而，在具有复杂基因组的生物体中，转基因插入位置的鉴定仍然是具有挑战性的。在这里，我们报告了一种基于纳米孔的方法来定位起源于玉米的DS转座元件在大豆基因组中的插入位置。在该方法中，使用寡核苷酸探针从转基因大豆植株的混合DNA样本中捕获含有DS元件的DNA片段。然后使用基于Minion的纳米孔平台对DS元素丰富的DNA进行测序。这种方法使我们能够通过一次测序快速定位51个转基因大豆品系中的D插入位置。这种策略具有高吞吐量、方便、可靠和成本效益高的特点。转基因等位基因定位协议可以很容易地翻译到其他具有复杂基因组的真核生物上。
Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes. Here, we report a nanopore-based method to map the insertion position of a Ds transposable element originating in maize in the soybean genome. In this method, an oligo probe is used to capture the DNA fragments containing the Ds element from pooled DNA samples of transgenic soybean plants. The Ds element-enriched DNAs are then sequenced using the MinION-based platform of Nanopore. This method allowed us to rapidly map the Ds insertion positions in 51 transgenic soybean lines through a single sequencing run. This strategy is high throughput, convenient, reliable, and cost-efficient. The transgenic allele mapping protocol can be easily translated to other eukaryotes with complex genomes.