tailieunhanh - Báo cáo y học: "Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. | Saintenac et al. Genome Biology 2011 12 R88 http 2011 12 9 R88 Genome Biology 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 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 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 .