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Resequencing Arabidopsis thaliana

拟南芥重测序

基本信息

批准号：
BB/F022697/1
负责人：
Richard Mott
金额：
$ 62万
依托单位：
University of Oxford
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2008
资助国家：
英国
起止时间：
2008 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FF022697%2F1
关键词：
Resequencing Arabidopsis thaliana

项目摘要

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 over 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 of the data use we need to know the genome sequence of each line. Fortunately we don't need to sequence each of the 1000 lines, which is too costly. Instead we can infer their sequences from the 19 founder genomes because we know the mosaic structure of each line. 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 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.

同一物种植物之间的差异，如开花时间、高度和叶色，可以部分解释它们的DNA序列之间的差异，这一事实可以用来识别导致农业中许多重要表型的基因。要做到这一点，一种方法需要一个遗传参考群体，这是一组相同物种(即真正繁殖的植物品种，每个品种内几乎没有遗传变异，但品种之间不同)的植物近交系，其基因组序列至少是近似地已知的，并在其上测量感兴趣的表型，如开花时间。然后，通过将观察到的不同品系之间的表型差异与它们的DNA序列之间的差异进行关联，有可能找到可能导致表型的DNA变化，从而确定负责的基因。由于所有开花植物都有共同的祖先和相似的基因，了解一种植物的功能通常可以转化为另一种植物。因此，通过利用一种简单的模式植物--拟南芥，它易于种植，世代时间短，有可能发现基因功能，然后将这些信息应用于重要的农业作物，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多个自交系。它们是通过反复杂交这种植物的19个现有品种而培育出来的，这些品种是从野外和世界各地收集的。这些品系已经进行了几代的近亲交配(称为自交)，直到每个品系都有一个固定的DNA序列，这是19个创始人的随机马赛克。每一条线都是一幅不同的马赛克。我们已经开始使用这些品系来寻找控制开花时间等性状的基因，但为了充分利用这些数据，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1000行中的每一行进行排序，这太昂贵了。相反，我们可以从19个创始人基因组中推断出它们的序列，因为我们知道每一条线的镶嵌结构。最近的技术进步使得以更低的成本和更快的速度对基因组进行排序成为可能。拟南芥的基因组长约1.2亿个碱基，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)，并公开这些数据。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品系中重要的功能变异。我们已经分发了这些品系，将它们的种子存放在A.thaliana储存中心，以便其他人可以使用这一资源。每一位创始人的基因组也将对进化论和种群遗传学的研究感兴趣。它们将由EBI的EnSembl Plants团队进行注释，并在EnSembl基因组浏览器上显示注释。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Mouse genomic variation and its effect on phenotypes and gene regulation.

DOI：
10.1038/nature10413
发表时间：
2011-09-14
期刊：
NATURE
影响因子：
64.8
作者：
Keane, Thomas M.;Goodstadt, Leo;Danecek, Petr;White, Michael A.;Wong, Kim;Yalcin, Binnaz;Heger, Andreas;Agam, Avigail;Slater, Guy;Goodson, Martin;Furlotte, Nicholas A.;Eskin, Eleazar;Nellaker, Christoffer;Whitley, Helen;Cleak, James;Janowitz, Deborah;Hernandez-Pliego, Polinka;Edwards, Andrew;Belgard, T. Grant;Oliver, Peter L.;McIntyre, Rebecca E.;Bhomra, Amarjit;Nicod, Jerome;Gan, Xiangchao;Yuan, Wei;van der Weyden, Louise;Steward, Charles A.;Bala, Sendu;Stalker, Jim;Mott, Richard;Durbin, Richard;Jackson, Ian J.;Czechanski, Anne;Guerra-Assuncao, Jose Afonso;Donahue, Leah Rae;Reinholdt, Laura G.;Payseur, Bret A.;Ponting, Chris P.;Birney, Ewan;Flint, Jonathan;Adams, David J.
通讯作者：
Adams, David J.

Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints.

DOI：
10.1093/molbev/mst166
发表时间：
2014-01
期刊：
Molecular biology and evolution
影响因子：
10.7
作者：
Bush SJ;Castillo-Morales A;Tovar-Corona JM;Chen L;Kover PX;Urrutia AO
通讯作者：
Urrutia AO

Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.

DOI：
10.1093/gbe/evr038
发表时间：
2011
期刊：
Genome biology and evolution
影响因子：
3.3
作者：
Lai AG;Denton-Giles M;Mueller-Roeber B;Schippers JH;Dijkwel PP
通讯作者：
Dijkwel PP

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana.

DOI：
10.1016/j.cell.2016.05.063
发表时间：
2016-07-14
期刊：
Cell
影响因子：
64.5
作者：
1001 Genomes Consortium. Electronic address: magnus.nordborg@gmi.oeaw.ac.at;1001 Genomes Consortium
通讯作者：
1001 Genomes Consortium

Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes.

DOI：
10.1016/j.cub.2011.07.002
发表时间：
2011-08-23
期刊：
Current biology : CB
影响因子：
0
作者：
Jiang C;Mithani A;Gan X;Belfield EJ;Klingler JP;Zhu JK;Ragoussis J;Mott R;Harberd NP
通讯作者：
Harberd NP