A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
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DOI：
10.1371/journal.pone.0019379
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发表时间：
2011-05-04
期刊：
影响因子：
3.7
通讯作者：
Mitchell SE
中科院分区：
文献类型：
--
作者：
Elshire RJ;Glaubitz JC;Sun Q;Poland JA;Kawamoto K;Buckler ES;Mitchell SE
下一代技术的进步已经将DNA测序的成本降低到了这样一个程度，即通过测序进行基因分型(GBS)现在对于高多样性、大基因组物种是可行的。在这里，我们报告了一种基于限制酶(RES)降低基因组复杂性来构建GBS文库的方法。这种方法简单、快速、极具特异性、高度重复性，并可能到达基因组的重要区域，而这些区域是序列捕获方法无法获得的。通过使用甲基化敏感的RES，可以避免基因组的重复区域，并以较低复制区为靶点，效率提高两到三倍。这极大地简化了具有高度遗传多样性的物种中具有计算挑战性的比对问题。GBS程序以玉米(IBM)和大麦(Oregon Wolfe Barley)重组自交系群体为例进行了演示，分别定位了大约200,000和25,000个序列标签。在像大麦这样缺乏完整基因组序列的物种中，一个优势是只需要在限制酶切位点周围开发参考图谱，这可以在样本基因分型过程中完成。在这种情况下，序列标记位置上的读取簇的共识成为参考。或者，对于在没有参考基因组的情况下的亲缘关系分析，可以简单地将序列标签视为显性标记。未来GBS在育种、保护和全球物种和种群调查中的应用可能允许植物育种者在新的种质或物种上进行基因组选择，而不必首先开发任何先前的分子工具，或者保护生物学家在不事先知道物种的基因组或多样性的情况下确定种群结构。
Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.
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影响因子：
48
作者：
Craig, David W.;Pearson, John V.;Szelinger, Szabolcs;Sekar, Aswin;Redman, Margot;Corneveaux, Jason J.;Pawlowski, Traci L.;Laub, Trisha;Nunn, Gary;Stephan, Dietrich A.;Homer, Nils;Huentelman, Matthew J.
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作者：
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