Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study.
Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study.
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DOI：
10.1007/s00438-017-1401-6
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发表时间：
2018-04
期刊：
影响因子：
--
通讯作者：
Pearce S
中科院分区：
文献类型：
--
作者：
Mo Y;Howell T;Vasquez-Gross H;de Haro LA;Dubcovsky J;Pearce S
诱导突变体植物群体的正向遗传筛选是鉴定感兴趣表型的基因的有力工具。使用传统技术，从正向筛选中定位致病突变是一个漫长的多步骤过程，需要鉴定广泛的遗传区域，然后进行候选基因测序以表征致病变体。通过全基因组测序的定位通过同时定义定位区域和提供关于诱导的遗传变异的信息来加速因果突变的鉴定。在小麦中，尽管高质量的基因组组装草图的可用性促进了作图和突变调用，但由于其庞大的基因组，全基因组重测序仍然非常昂贵。在目前的研究中，我们使用外显子组测序作为降低复杂性的策略来检测与靶表型相关的突变。在一个分离的小麦EMS群体中，我们确定了一个明确的峰值区域染色体臂4 BS与植株高度增加。虽然没有显著的SNP似乎是突变表型的原因，但它们足以鉴定包含9个基因的连锁~ 1.9 Mb缺失。这些基因包括Rht-B1，已知它对植物高度有很强的影响，是观察到的表型的强有力的候选者。我们进行了模拟实验，以确定测序深度和批量大小的影响，并讨论在设计小麦测序实验时考虑每个因素的重要性。这种方法可以加速识别候选的因果点突变或连锁缺失的重要表型。本文的在线版本（10.1007/s 00438 -017-1401-6）包含补充材料，可供授权用户使用。
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes. The online version of this article (10.1007/s00438-017-1401-6) contains supplementary material, which is available to authorized users.
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