High-throughput genotyping by whole-genome resequencing
High-throughput genotyping by whole-genome resequencing
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DOI：
10.1101/gr.089516.108
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发表时间：
2009-06-01
期刊：
影响因子：
7
通讯作者：
Han, Bin
中科院分区：
文献类型：
--
作者：
Huang, Xuehui;Feng, Qi;Han, Bin
下一代测序技术加上越来越多的基因组序列为重新设计基因分型策略提供了机会，以实现更有效的遗传作图和基因组分析。我们开发了一种利用Illumina基因组分析仪产生的全基因组重测序数据对重组群体进行基因分型的高通量方法。设计了滑动窗口方法来集体检查全基因组单核苷酸多态性，用于基因型调用和重组断点确定。利用该方法构建了150个水稻重组自交系的遗传图谱，基因型识别的准确率为99.94%，重组断裂点的分辨率平均在40 kb以内。与用287个基于PCR的标记构建的水稻群体遗传图谱相比，基于测序的方法在数据收集方面更快203，在重组断点确定方面更精确353。利用基于测序的遗传图谱，我们在水稻“绿色革命”基因的100 kb区域内定位了一个对株高影响较大的数量性状位点。通过计算机模拟，我们证明该方法对于来自基因组序列质量可变的生物的不同类型的作图群体具有鲁棒性，并且对于基因组大小较大且多态性较低的生物是可行的。随着测序技术的不断进步，这种基于基因组的方法可能取代传统的基于标记的基因分型方法，为大规模基因发现和解决广泛的生物学问题提供强有力的工具。
The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was; 203 faster in data collection and 353 more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution'' gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.