Targeted re-sequencing of the allohexaploid wheat exome
Targeted re-sequencing of the allohexaploid wheat exome
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DOI：
10.1111/j.1467-7652.2012.00713.x
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发表时间：
2012-08-01
影响因子：
13.8
通讯作者：
Edwards, Keith J.
中科院分区：
文献类型：
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作者：
Winfield, Mark O.;Wilkinson, Paul A.;Edwards, Keith J.
小麦（Triticum aestivum）是由A、B和D三个不同祖先基因组组成的异源六倍体。小麦基因组的多倍体性质及其大的尺寸限制了我们产生全基因组研究所需的大量序列数据的能力。即使随着下一代测序技术的出现，在任何时候为几个以上的小麦基因组生成全基因组序列仍然相对昂贵。为了克服这个问题，我们已经开发了一种基于NimbleGen阵列技术的靶向捕获再测序方案，以捕获和表征56.5 Mb的基因组DNA，其序列与来自8个不同的英国异源六倍体小麦品种的100 000多个转录本相似。使用这个程序结合精心设计的生物信息学程序，我们已经确定了超过50万个推定的单核苷酸多态性（SNP）。虽然80%的这些之间的同源异形体基因组，A，B和D的变体，一个显着的数字（20%）之间的8个品种研究的推定品种SNP。后者的一小部分多态性使用KASPar技术进行了实验验证，94%被证明是真实的。这里描述的程序测序小麦基因组的大部分，和各种SNPs确定应该是相当大的使用更广泛的小麦社区。
Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of sequence data required for whole genome studies. Even with the advent of next-generation sequencing technology, it is still relatively expensive to generate whole genome sequences for more than a few wheat genomes at any one time. To overcome this problem, we have developed a targeted-capture re-sequencing protocol based upon NimbleGen array technology to capture and characterize 56.5 Mb of genomic DNA with sequence similarity to over 100 000 transcripts from eight different UK allohexaploid wheat varieties. Using this procedure in conjunction with a carefully designed bioinformatic procedure, we have identified more than 500 000 putative single-nucleotide polymorphisms (SNPs). While 80% of these were variants between the homoeologous genomes, A, B and D, a significant number (20%) were putative varietal SNPs between the eight varieties studied. A small number of these latter polymorphisms were experimentally validated using KASPar technology and 94% proved to be genuine. The procedures described here to sequence a large proportion of the wheat genome, and the various SNPs identified should be of considerable use to the wider wheat community.