Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome.
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome.
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DOI：
10.1186/gb-2011-12-9-r88
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发表时间：
2011-09-14
期刊：
影响因子：
12.3
通讯作者：
Akhunov ED
中科院分区：
文献类型：
--
作者：
Saintenac C;Jiang D;Akhunov ED
草种适应各种生境的能力归因于其基因组的动态性质，这些基因组是由多轮古代和现代多倍化形成的。为了更好地了解多倍体基因组功能相关区域变异的性质和程度，我们开发了一种序列捕获测定法来比较异源四倍体小麦种质的外显子序列。设计了一种序列捕获测定法，用于对来自异源四倍体小麦的总共3，497个基因的3.5 Mb外显子区域进行靶向重测序。这些数据用于描述编码区的SNPs、拷贝数变异和同源序列差异。在多倍体基因组中的变异发现的程序开发和实验验证。约1%和24%的SNP分别为功能丧失和非同义突变。在参与翻译和代谢的几组基因中发现了替代突变的代表性不足。在栽培小麦中，基因重复占主导地位，而在野生小麦中，基因缺失比重复多。我们证明，即使靶向多倍体基因组和捕获诱饵之间的序列相似性水平可以使富集效率发生偏差，外显子捕获也是多倍体中变体发现的有力方法。我们的研究结果表明，异源多倍体小麦可以在编码区以较高的速率积累新的变异。这一过程有可能扩大功能多样性并产生新的表型变异，最终在新的适应性和重要农艺性状的起源中发挥关键作用。
The ability of grass species to adapt to various habitats is attributed to the dynamic nature of their genomes, which have been shaped by multiple rounds of ancient and recent polyploidization. To gain a better understanding of the nature and extent of variation in functionally relevant regions of a polyploid genome, we developed a sequence capture assay to compare exonic sequences of allotetraploid wheat accessions. A sequence capture assay was designed for the targeted re-sequencing of 3.5 Mb exon regions that surveyed a total of 3,497 genes from allotetraploid wheat. These data were used to describe SNPs, copy number variation and homoeologous sequence divergence in coding regions. A procedure for variant discovery in the polyploid genome was developed and experimentally validated. About 1% and 24% of discovered SNPs were loss-of-function and non-synonymous mutations, respectively. Under-representation of replacement mutations was identified in several groups of genes involved in translation and metabolism. Gene duplications were predominant in a cultivated wheat accession, while more gene deletions than duplications were identified in wild wheat. We demonstrate that, even though the level of sequence similarity between targeted polyploid genomes and capture baits can bias enrichment efficiency, exon capture is a powerful approach for variant discovery in polyploids. Our results suggest that allopolyploid wheat can accumulate new variation in coding regions at a high rate. This process has the potential to broaden functional diversity and generate new phenotypic variation that eventually can play a critical role in the origin of new adaptations and important agronomic traits.
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影响因子：
4.4
作者：
Akhunov ED;Akhunova AR;Anderson OD;Anderson JA;Blake N;Clegg MT;Coleman-Derr D;Conley EJ;Crossman CC;Deal KR;Dubcovsky J;Gill BS;Gu YQ;Hadam J;Heo H;Huo N;Lazo GR;Luo MC;Ma YQ;Matthews DE;McGuire PE;Morrell PL;Qualset CO;Renfro J;Tabanao D;Talbert LE;Tian C;Toleno DM;Warburton ML;You FM;Zhang W;Dvorak J
通讯作者：
Dvorak J
影响因子：
3.7
作者：
Bansal, Vikas;Tewhey, Ryan;Schork, Nicholas J.
通讯作者：
Schork, Nicholas J.
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S
影响因子：
56.9
作者：
Clark, Richard M.;Schweikert, Gabriele;Weigel, Detlef
通讯作者：
Weigel, Detlef
DOI：
10.1073/pnas.87.24.9640
发表时间：
1990-12-01
影响因子：
11.1
作者：
DVORAK, J;ZHANG, HB
通讯作者：
ZHANG, HB