Resequencing Arabidopsis thaliana

拟南芥重测序

• 批准号: BB/F019793/1
• 负责人: Ewan Birney
• 金额: $ 23.29万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FF019793%2F1
• 关键词: Resequencing; Arabidopsis; thaliana

Describe the proposed research in simple terms in a way that could be publicised to a general audience [up to 4000 chars] Variation, such as flowering time, height and leaf colour between plants of the same species can be explained in part by differences between their DNA sequences, and this fact can be used to identify genes responsible for many phenotypes of importance in agriculture. One way of doing this this requires a genetic reference population, which is a set of inbred lines of plants of the same species (ie varieties of plants that breed true and contain little or no genetic variation within each variety but which differ between varieties) whose genome sequences are known, at least approximately, and on which the phenotype of interest, such as flowering time, is measured. Then by correlating the differences observed between the phenotypes measured across the lines with differences between their DNA sequences, it is possible to find DNA changes that may be responsible for the phenotypes, and hence identify the responsible genes. Because all flowering plants have a common ancestor and share similar genes, understanding the function in one plant species can often be translated to another. Therefore by working with a simple model plant, the thale cress Arabidopsis Thaliana, which is easy to grow and has a short generation time, it is possible to discover gene function and then apply this information to agriculturally important crops, to improve yields to the benefit of mankind. We have developed a reference population of 763 Arabidopsis inbred lines, shortly to be expanded to ober 1000 lines. They have been bred by repeatedly crossing 19 existing varieties of this plant that were collected from the wild and from across the world. The lines have been inbred (called 'selfing') for several generations until each line has a fixed DNA sequence which is a random mosaic of the 19 founders. Each line is a different mosaic. We have begun to use these lines to find the genes responsible for traits such as flowering time, but in order to make the best use we need to know the genome sequence of each line. Fortunately we don't need to sequence each of the 763 lines, which is costly. Instead we can infer their sequences from the 19 founder genomes because we know the mosaic structure of the 763. Recent technological improvements make it possible to sequence genomes much more cheaply and quickly. The genome of Arabidopsis Thaliana is about 120 million bases long and can now be sequenced in about a day. We propose to sequence the genomes of 17 founders (the other two genomes are already sequenced) and make this data publicly available. We will develop software and statistical methods so that DNA variation between the 19 genomes can be used to help identify functionally important variations in the 763 lines. We have already distributed the lines by depositing their seeds in the A. thaliana stock centre so that others can use this resource. The genomes of each of the founders will also be of interest for studies of evolution and population genetics. They will be annotated by the Ensembl Plants team at EBI and the annotations displayed on the Ensembl genome browser.

用简单的术语描述拟议的研究，以便向普通观众宣传[最多4000个字符]同一物种植物之间的开花时间，高度和叶子颜色的变化可以部分地通过它们的DNA序列之间的差异来解释，这一事实可以用来识别负责农业中许多重要表型的基因。这样做的一种方法是需要一个遗传参考群体，这是一组相同物种的植物近交系（即繁殖真实并且在每个品种内包含很少或没有遗传变异但在品种之间不同的植物品种），其基因组序列至少是近似已知的，并且在其上测量感兴趣的表型，例如开花时间。然后，通过将跨品系测量的表型之间观察到的差异与它们的DNA序列之间的差异相关联，可以找到可能导致表型的DNA变化，从而鉴定出负责的基因。由于所有开花植物都有一个共同的祖先，并共享相似的基因，因此了解一种植物物种的功能通常可以翻译到另一种植物物种。因此，通过简单的模式植物，即易于生长且世代时间短的塔勒水芹拟南芥，有可能发现基因功能，然后将这些信息应用于农业上重要的作物，以提高产量，造福人类。我们已经建立了763个拟南芥自交系的参考群体，不久将扩大到1000多个品系。它们是通过反复杂交从野生和世界各地收集的19种现有的这种植物品种而培育出来的。这些品系已经近交（称为“自交”）了几代，直到每个品系都有一个固定的DNA序列，这是19个创始人的随机嵌合体。每条线都是不同的马赛克。我们已经开始使用这些品系来寻找负责开花时间等性状的基因，但为了最好地利用这些基因，我们需要知道每个品系的基因组序列。幸运的是，我们不需要对763行中的每一行进行排序，这是昂贵的。相反，我们可以从19个创始人基因组中推断出它们的序列，因为我们知道763的镶嵌结构。最近的技术进步使得更便宜和更快地对基因组进行测序成为可能。拟南芥的基因组大约有1.2亿个碱基长，现在可以在大约一天内完成测序。我们建议对17位创始人的基因组进行测序（另外两个基因组已经测序），并将这些数据公开。我们将开发软件和统计方法，以便19个基因组之间的DNA变异可以用来帮助识别763个品系中的重要功能变异。我们已经通过将种子存放在A. thaliana股票中心，以便其他人可以使用这一资源。每个创始人的基因组也将对进化和群体遗传学的研究感兴趣。它们将由EBI的Ensembl Plants团队进行注释，注释将显示在Ensembl基因组浏览器上。

项目成果

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

• DOI: 10.1038/nature10414
• 发表时间: 2011-08-28
• 期刊: Nature
• 影响因子: 64.8
• 作者: Gan X;Stegle O;Behr J;Steffen JG;Drewe P;Hildebrand KL;Lyngsoe R;Schultheiss SJ;Osborne EJ;Sreedharan VT;Kahles A;Bohnert R;Jean G;Derwent P;Kersey P;Belfield EJ;Harberd NP;Kemen E;Toomajian C;Kover PX;Clark RM;Rätsch G;Mott R
• 通讯作者: Mott R

Ensembl Genomes: extending Ensembl across the taxonomic space.

• DOI: 10.1093/nar/gkp871
• 发表时间: 2010-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kersey PJ;Lawson D;Birney E;Derwent PS;Haimel M;Herrero J;Keenan S;Kerhornou A;Koscielny G;Kähäri A;Kinsella RJ;Kulesha E;Maheswari U;Megy K;Nuhn M;Proctor G;Staines D;Valentin F;Vilella AJ;Yates A
• 通讯作者: Yates A

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

• DOI: 10.1093/nar/gkr895
• 发表时间: 2012-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kersey PJ;Staines DM;Lawson D;Kulesha E;Derwent P;Humphrey JC;Hughes DS;Keenan S;Kerhornou A;Koscielny G;Langridge N;McDowall MD;Megy K;Maheswari U;Nuhn M;Paulini M;Pedro H;Toneva I;Wilson D;Yates A;Birney E
• 通讯作者: Birney E

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

• DOI: 10.1093/database/bar030
• 发表时间: 2011
• 期刊: Database : the journal of biological databases and curation
• 作者: Kinsella RJ;Kähäri A;Haider S;Zamora J;Proctor G;Spudich G;Almeida-King J;Staines D;Derwent P;Kerhornou A;Kersey P;Flicek P
• 通讯作者: Flicek P