Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat
Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat
复制标题
整合基因组资源，提供面包小麦的完整基因和启动子捕获探针组
DOI：
10.1101/363663
复制
发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Gardiner L
中科院分区：
文献类型：
--
作者：
Gardiner L
背景小麦基因组鸟枪式重测序费用昂贵，因为它的大而重复的基因组。此外，序列数据可能无法唯一地映射到参考基因组，因此很难明确地分配变异。利用靶标捕获进行再测序，可以在高覆盖率下对大量个体进行测序，从而可靠地识别与重要农艺性状相关的变异。结果我们提出并验证了两套六倍体面包小麦的黄金标准捕获探针，一套基因和一套启动子捕获，它们是利用最近开发的基因组序列和注释资源设计的。这些捕获可以组合在一起，也可以单独使用。我们证明，捕获探针集有效地丰富了基因组中鉴定的高置信度基因和启动子，以及很大比例的低置信度基因和启动子。最后，我们展示了成功的样本多路复用，它可以为SNP调用产生足够的序列覆盖，同时显著降低捕获基因和启动子的每个样本的成本。结论我们表明，采用‘孤岛策略’的捕获设计可以用2×160Mb的探针组来分析小麦的大基因/启动子空间。此外，这些分析将小麦基因组的区域扩展到其外显子组之外的区域，为在大群体中详细描述这些调控区域提供了工具。
BackgroundWhole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.ResultsWe present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.ConclusionsWe show that a capture design employing an ‘island strategy’ can enable analysis of the large gene/promoter space of wheat with only 2×160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.