Tool for finding linked genetic polymorphisms in reference-less complex plant genomes from unassembled next-generation reads.

用于从未组装的下一代读数中查找无参考复杂植物基因组中连锁遗传多态性的工具。

• 批准号: BB/I024174/1
• 负责人: Mario Caccamo
• 金额: $ 1.37万
• 依托单位: Earlham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI024174%2F1
• 关键词: Tool; finding; linked; genetic; polymorphisms

Differences in the genome of individuals of the same species, called polymorphisms, are the genetic basis of traits such as resistance or susceptibility to disease. By identifying polymorphisms it is possible to pinpoint either the agents of resistance or susceptibility or at the least locate regions on the genome that are placed nearby and can act as positional markers that can be associated with the trait of interest. Many wild populations of plant species that are closely related to domesticated varieties important for food and industry are resistant to common diseases that could potentially devastate important crops across the world. Combating these diseases chemically is both costly and environmentally damaging so breeding varieties that are resistant is absolutely necessary for food security. Genetic methods for identifying markers are time consuming and require large amounts of expensive and slow laboratory work. New methods in high-throughput DNA sequencing are able to comprehensively sample entire genomes at an affordable cost. These technologies return many millions of small fragments not a continuous sequence. The volumes of data generated by the NGS instruments has resulted in the need for new methods to assemble the fragments or align to an existing, previously assembled reference sequence. Currently, polymorphism identification relies on having some sort of reference to which sequence reads can be aligned. Aligned reads are then examined for consensus differences to the reference that indicate a genetic difference between the genome of that sampled in the reads and the reference. Naturally this is only possible where a reference genome exists. Since the creation of even a rough draft genome sequence can take many months, the detection of polymorphisms specifying resistance to diseases in relatives to agriculturally important organisms that have no such reference becomes a massively time consuming and difficult task. When reference sequence is available identifying polymorphisms among many individuals from a population, to associate genotypes with specific phenotypes for example, require many cycles of alignment and comparison. Our objective is to develop a tool that takes advantage of the recent developments in high-throughput DNA sequencing and new computational methods to identify polymorphisms between multiple sources without the need for comparison with a reference sequence. These methods will allow us to detect genetic variants directly from the raw sequences reads without the requirement of a reference genome. The time required would be on the order of hours, rather than months or years in the case where assembly may be required. The tool will produce short but useful genomic mini-assemblies with embedded polymorphisms that can be utilised by bench workers for downstream experiments. We will be able to provide ranking of SNPs and classifications based on the provenance of different reads, for example detecting SNPs common to individuals with a trait. The tool will be an important addition to the repertoire of methods available to bioinformaticians involved in polymorphism detection and could invaluable to projects without an available reference sequence. The tool will also prove useful to bioinformaticians with a reference sequence, we will be able to remove the need for many sequential alignments to a reference and compress subsequent polymorphism detection into a single step.

同一物种的个体基因组的差异，称为多态性，是诸如对疾病的抵抗力或易感性等性状的遗传基础。通过鉴定多态性，可以精确定位抗性或易感性的因子，或者至少定位基因组上位于附近的区域，并且可以作为与感兴趣的性状相关的位置标记。许多与对粮食和工业重要的驯化品种密切相关的植物物种的野生种群对可能使世界各地的重要作物遭受潜在危害的常见疾病具有抗性。用化学方法防治这些疾病既昂贵又破坏环境，因此培育抗病品种对粮食安全绝对必要。用于鉴定标记的遗传方法是耗时的，并且需要大量昂贵且缓慢的实验室工作。高通量DNA测序的新方法能够以可承受的成本全面地对整个基因组进行采样。这些技术返回数百万个小片段，而不是连续的序列。NGS仪器产生的大量数据导致需要新的方法来组装片段或与现有的先前组装的参考序列进行比对。目前，多态性鉴定依赖于具有某种序列读段可以比对的参考。然后检查比对的读段与参考的共有差异，所述共有差异指示读段中取样的基因组与参考之间的遗传差异。当然，这只有在存在参考基因组的情况下才有可能。由于即使是粗略的基因组序列草图的创建也可能需要数月，因此检测指定农业上重要的生物体的亲属中对疾病的抗性的多态性（没有这种参考）变得非常耗时且困难。当参考序列可用于鉴定来自群体的许多个体中的多态性时，例如，为了将基因型与特定表型相关联，需要许多比对和比较循环。我们的目标是开发一种工具，利用高通量DNA测序和新的计算方法的最新发展，以确定多个来源之间的多态性，而不需要与参考序列进行比较。这些方法将使我们能够直接从原始序列读数中检测遗传变异，而不需要参考基因组。在可能需要组装的情况下，所需的时间将是几个小时，而不是几个月或几年。该工具将产生短但有用的基因组微型组装，其中嵌入了多态性，可供实验室工作人员用于下游实验。我们将能够根据不同读段的来源提供SNP的排名和分类，例如检测具有某种性状的个体所共有的SNP。该工具将是参与多态性检测的生物信息学家可用方法库的重要补充，对于没有可用参考序列的项目可能非常宝贵。该工具也将被证明是有用的生物信息学家与参考序列，我们将能够消除需要许多序列比对的参考和压缩到一个单一的步骤，随后的多态性检测。

项目成果

Reference-free SNP detection: dealing with the data deluge.

• DOI: 10.1186/1471-2164-15-s4-s10
• 发表时间: 2014
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Leggett RM;MacLean D
• 通讯作者: MacLean D