Mapping the zebra finch genome

斑马雀是一种雀类或鸣禽。雀类在广泛的生物学学科中得到了广泛的研究，无论是作为实验室模式生物还是在野外。在实验室里，它们被用来理解歌曲是如何发展、控制和学习的，也是理解其他物种发声的模式系统。对野生雀形目鸟类种群的研究促进了我们对自然选择、性选择、近亲交配的影响、物种形成机制、进化停滞的原因以及与适应相关的性状的遗传结构的理解。近年来，通过对有血统的种群进行定量遗传分析，在这些问题上取得了巨大的进展。令人沮丧的是，雀形目动物的基因组资源没有许多其他脊椎动物那么发达。因此，目前在雀形目动物中进行基因图谱研究几乎是不可能的，许多生物学家认为这一方向是先前工作的下一个合乎逻辑的延伸。然而，现在出现了解决这个问题的机会，因为斑马雀的基因组目前正在进行测序。这将是雀形目动物物种的第一个基因组序列，也是鸟类中的第二个基因组序列；第一个鸡基因组组合草案于2004年发布，但加利弗斯(包括鸡在内的群体)和雀形目鸟类在大约1亿年前就出现了分歧。在这个项目中，我们将使用谢菲尔德长期研究种群中的鸟类，建立斑马雀基因组的遗传连锁图谱。该项目是由三件事促成的：(I)斑马雀基因组序列的可获得性，这将使我们能够快速找到要放在地图上的遗传标记；(Ii)我们的多代斑纹草雀种群；(Iii)新的高通量基因分型平台，它可以产生以前不可能的规模的数据。与旧的方法相比，新平台产生数据的成本降低了5-10倍，速度至少提高了5-10倍。斑马雀连锁图有几个用途。首先，它将被用来帮助“组装”斑马雀的基因组序列。测序程序通常会产生大的重叠序列，但将它们按正确的顺序放置在正确的染色体上是非常困难的。如果可以参考连锁图谱，这项任务就会变得简单得多，因为连锁图谱中的标记是沿着染色体排序的。其次，我们将使用该图谱来测试一些群体遗传假说，特别是那些与染色体重排和减数分裂重组率的进化有关的假说。第三，该图谱代表了一种资源，可以用来识别导致一些重要表型变异的基因，包括精子的活力和形态、身体状况、羽毛强度和歌唱表现。最后，该图谱可以用来开始在其他雀形目动物物种中建立类似的图谱，特别是那些基因图谱是一个有吸引力的未来方向的物种，比如那些已经成为野生长期生态学研究对象的物种。很好的例子包括牛津威瑟姆森林的大量山雀，以及瑞典哥特兰岛上的衣领捕蝇器。

Zebra finches (Taeniopygia guttata) are a passerine or songbird. Passerines are widely studied in a broad range of biological disciplines, both as laboratory model organisms, and in the wild. In the laboratory they are used to understand how song is developed, controlled and learned, and are a model system for understanding vocalisation in other species. Studies of wild passerine populations have advanced our understanding of natural selection, sexual selection, the effects of inbreeding, mechanisms of speciation, the causes of evolutionary stasis, and the genetic architecture of fitness-related traits. Enormous progress on many of these questions has been made in recent years by quantitative genetic analyses of pedigreed populations. Frustratingly, genomics resources are less well-developed for passerines than many other vertebrate taxa. As a result it is currently almost impossible to carry out gene mapping studies in passerines, a direction that many biologists feel is the next logical extension of previous work. However, an opportunity has now arisen to address this problem because the zebra finch genome is currently being sequenced. This will be the first genome sequence for a passerine species, and only the second of any bird; a first draft chicken genome assembly was released in 2004, but Galliforms (the group that includes chickens) and passerines diverged ~100 million years ago. In this project we will build a genetic linkage map of the zebra finch genome, using birds from a long-term study population maintained in Sheffield. The project is made possible by three things: (i) the availability of the zebra finch genome sequence, which will enable us to rapidly find genetic markers to put on the map, (ii) our multigenerational zebra finch population and (iii) new high-throughput genotyping platforms that can produce data on a scale that was not previously possible. Compared to older methods the new platforms produce data at 5-10 times lower cost and at least 5-10 times more rapidly. The zebra finch linkage map will serve several purposes. First, it will be used to help 'assemble' the zebra finch genome sequence. Sequencing programs typically produce large, overlapping sequences, but placing them in the correct order and on the correct chromosomes is very difficult. The task is made much simpler if reference can be made to a linkage map, where markers are ordered along the chromosomes. Second, we will use the map to test a number of population genetic hypotheses, particularly those relating to the evolution of chromosomal rearrangements and meiotic recombination rates. Third, the map represents a resource which can be used to identify the genes that are responsible for variation in a number of important phenotypes including sperm motility and morphology, body condition, plumage intensity and song performance. Finally, the map can be used to start building similar maps in other passerine species, especially those where gene mapping is an attractive future direction, such as those that have been the subject of long-term ecological studies in the wild. Good examples include the great tit population at Wytham Woods, Oxford and the collared flycatchers on the Swedish island of Gotland.