Resequencing Arabidopsis thaliana

相同物种植物之间的差异，如开花时间、高度和叶子颜色，可以部分地用它们的DNA序列的差异来解释，这一事实可以用来识别对农业中许多重要表型负责的基因。实现这一目标的一种方法是需要一个遗传参考种群，这是一组相同物种的植物自交系（即繁殖真实的植物品种，每个品种中含有很少或没有遗传变异，但品种之间存在差异），它们的基因组序列是已知的，至少是近似的，并且对感兴趣的表型（如开花时间）进行测量。然后，通过将观察到的表型差异与它们的DNA序列之间的差异相关联，就有可能找到可能导致表型的DNA变化，从而确定负责基因。因为所有的开花植物都有一个共同的祖先和相似的基因，所以了解一种植物的功能通常可以转化为另一种植物。因此，通过研究一种简单的模式植物——拟南芥（Arabidopsis Thaliana），这种植物易于种植，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，以提高产量，造福人类。我们已经开发了一个763个拟南芥自交系的参考群体，不久将扩展到1000多个系。它们是通过从野外和世界各地收集的这种植物的19个现有品种反复杂交而培育出来的。这些品系经过几代的近亲繁殖（称为“自交”），直到每个品系都有一个固定的DNA序列，这是19个始祖随机拼接而成的。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与开花时间等性状有关的基因，但为了充分利用数据，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个创始者基因组中推断出它们的序列，因为我们知道每条染色体的镶嵌结构。最近的技术进步使得基因组测序变得更加廉价和快速。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，这样19个基因组之间的DNA变异就可以用来帮助识别细胞系中功能上重要的变异。我们已经将这些品种的种子存放在拟南芥库存中心，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植物团队进行注释，并在Ensembl基因组浏览器上显示注释。

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.