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Mapping the zebra finch genome

绘制斑胸草雀基因组图谱

基本信息

批准号：
BB/E017509/1
负责人：
J Slate
金额：
$ 71.82万
依托单位：
University of Sheffield
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2007
资助国家：
英国
起止时间：
2007 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FE017509%2F1
关键词：
Mapping zebra finch genome

项目摘要

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.

斑胸草雀（Taeniopygia guttata）是雀形目或鸣禽。雀形目在广泛的生物学科中被广泛研究，无论是作为实验室模式生物，还是在野外。在实验室中，它们被用来理解歌曲是如何发展、控制和学习的，并且是理解其他物种发声的模型系统。对野生雀形目种群的研究促进了我们对自然选择、性选择、近亲繁殖的影响、物种形成机制、进化停滞的原因以及与适应性相关的性状的遗传结构的理解。近年来，通过对纯种种群的定量遗传分析，在许多问题上取得了巨大的进展。令人沮丧的是，雀形目的基因组学资源不如许多其他脊椎动物类群发达。因此，目前几乎不可能在雀形目中进行基因定位研究，许多生物学家认为这是以前工作的下一个逻辑延伸。然而，现在出现了解决这个问题的机会，因为斑马雀基因组目前正在测序。这将是雀形目物种的第一个基因组序列，也是所有鸟类的第二个基因组序列;第一份鸡基因组组装草案于2004年发布，但鸡形目（包括鸡的类群）和雀形目在约1亿年前就出现了分歧。在这个项目中，我们将建立一个遗传连锁图谱的斑胸草雀基因组，从一个长期的研究人口保持在谢菲尔德的鸟类。该项目是由三件事：（i）斑马雀基因组序列的可用性，这将使我们能够快速找到遗传标记放在地图上，（ii）我们的多代斑马雀种群和（iii）新的高通量基因分型平台，可以产生以前不可能的规模数据。与旧方法相比，新平台以低5-10倍的成本和至少5-10倍的速度生成数据。斑胸草雀的连锁图谱有几个用途。首先，它将被用来帮助“组装”斑胸草雀的基因组序列。测序程序通常产生大的重叠序列，但将它们以正确的顺序放置在正确的染色体上是非常困难的。如果可以参照连锁图，标记是沿染色体沿着的，那么这项工作就简单多了。第二，我们将使用该图谱来检验一些群体遗传学假设，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设。第三，该图谱代表了一种资源，可用于识别负责许多重要表型（包括精子活力和形态、身体状况、羽毛强度和歌唱表现）变异的基因。最后，该图谱可用于在其他雀形目物种中开始构建类似的图谱，特别是那些基因图谱是一个有吸引力的未来方向的物种，例如那些长期在野外进行生态研究的物种。很好的例子包括牛津Wytham Woods的大山雀种群和瑞典哥特兰岛的领蝇。

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）

Evolutionary analysis and expression profiling of zebra finch immune genes.

DOI：
10.1093/gbe/evq061
发表时间：
2010
期刊：
Genome biology and evolution
影响因子：
3.3
作者：
Ekblom R;French L;Slate J;Burke T
通讯作者：
Burke T

A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).

DOI：
10.1186/1471-2164-11-218
发表时间：
2010-04-01
期刊：
BMC genomics
影响因子：
4.4
作者：
Ball AD;Stapley J;Dawson DA;Birkhead TR;Burke T;Slate J
通讯作者：
Slate J

A comparison of synteny and gene order on the homologue of chicken chromosome 7 between two passerine species and between passerines and chicken.

两种雀形目鸟类以及雀形目动物和鸡之间鸡7号染色体同源物的同线性和基因顺序比较。

DOI：
10.1159/000125837
发表时间：
2008
期刊：
Cytogenetic and genome research
影响因子：
1.7
作者：
Hale MC
通讯作者：
Hale MC

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.

DOI：
10.1155/2012/281693
发表时间：
2012
期刊：
Comparative and functional genomics
影响因子：
0
作者：
Ekblom R;Slate J;Horsburgh GJ;Birkhead T;Burke T
通讯作者：
Burke T

High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.

DOI：
10.1186/1471-2164-14-176
发表时间：
2013-03-15
期刊：
BMC genomics
影响因子：
4.4
作者：
Dawson DA;Ball AD;Spurgin LG;Martín-Gálvez D;Stewart IR;Horsburgh GJ;Potter J;Molina-Morales M;Bicknell AW;Preston SA;Ekblom R;Slate J;Burke T
通讯作者：
Burke T