targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome有针对性的分析核苷酸和拷贝数变异的外显子捕获异源四倍体小麦基因组中.pdfVIP

Saintenac et al. Genome Biology 2011, 12:R88 /2011/12/9/R88 RESEARCH Open Access Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome * Cyrille Saintenac, Dayou Jiang and Eduard D Akhunov Abstract Background: 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. Results: 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. Conclusions: 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 a